Conda problems: Failed to activate conda environment
Hi All I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working) Conda problem: Failed to activate conda environment. Conda works during tool installation or reinstallation. Galaxy tools have been updated/reinstalled so they all look "green" in manage tools. In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean. When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster. The galaxy application raised errors like the two below. "Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C" " Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. " Galaxy started and stopped using supervisord with config below: Thanks, hopefully someone has seen this before ... regards, Gerhard [program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT [program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true [group:galaxy] programs = handler, web [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
Hi Gerhard, it seems your tool is picking up the old tool_dependency version and not the conda version of python. Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers... to configure the order of dependency resolution in Galaxy. Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer > Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule <http://www.sun.ac.za/emaildisclaimer >
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Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on. Take for example the trim_galore tool. The error is /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found And the script is: #!/bin/bash # The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi In fact most of the tools do this post-upgrade - where they cannot find a file. Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts. Any ideas how we should go about finding this error? Thanks, Gerhard PS Here is the hisat2 output. #!/bin/bash # The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat' The job fails when it cannot find “hisat2-build”. Fatal error: Exit code 127 () /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh): PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR The conda environment with dependencies seems to be there: /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org ________________________________ From: Björn Grüning <bjoern.gruening@gmail.com> Sent: 05 July 2018 22:00:58 To: Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard, it seems your tool is picking up the old tool_dependency version and not the conda version of python. Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers... [https://avatars0.githubusercontent.com/u/7937847?s=400&v=4]<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> galaxyproject/galaxy<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone. to configure the order of dependency resolution in Galaxy. Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer > Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule <http://www.sun.ac.za/emaildisclaimer >
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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Hi, can you do: . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 And see if you can execute trim_galore from the commandline and get the help? Ciao, Bjoern Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer > Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule <http://www.sun.ac.za/emaildisclaimer >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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Hi - tx for (fast) reply. Ok ... with this result ... (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found Environment is: (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env XDG_SESSION_ID=45352 HOSTNAME=storage1.hpc SELINUX_ROLE_REQUESTED= TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=10.55.40.3 55438 22 PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5: SELINUX_USE_CURRENT_RANGE= QTDIR=/usr/lib64/qt-3.3 OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0 QTINC=/usr/lib64/qt-3.3/include PERL_MB_OPT=--install_base /root/perl5 SSH_TTY=/dev/pts/2 QT_GRAPHICSSYSTEM_CHECKED=1 USER=root LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: MAIL=/var/spool/mail/root PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 CONDA=/home/.galaxy/tooldeps/_conda PWD=/home/.galaxy/tooldeps/_conda/envs LANG=en_ZA.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles LOADEDMODULES= KDEDIRS=/usr PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] SELINUX_LEVEL_REQUESTED= HISTCONTROL=ignoredups SHLVL=1 HOME=/root CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] PERL_LOCAL_LIB_ROOT=:/root/perl5 LOGNAME=root QTLIB=/usr/lib64/qt-3.3/lib SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/0 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins PERL_MM_OPT=INSTALL_BASE=/root/perl5 XAUTHORITY=/tmp/.Xauthority.root BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ ________________________________ From: Björn Grüning <bjoern.gruening@gmail.com> Sent: 10 July 2018 08:38:15 To: Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi, can you do: . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 And see if you can execute trim_galore from the commandline and get the help? Ciao, Bjoern Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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Which means that your conda envs are not what they are supposed to be. You can fix this by removing the folder and let Galaxy re-created them, but you should figure out why they are "empty". Maybe a wrong channel priority or network issues during installation? Hope that helps. You could also from insite the env, do a `conda install ...`
Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found
Environment is:
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env XDG_SESSION_ID=45352 HOSTNAME=storage1.hpc SELINUX_ROLE_REQUESTED= TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=10.55.40.3 55438 22 PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5: SELINUX_USE_CURRENT_RANGE= QTDIR=/usr/lib64/qt-3.3 OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0 QTINC=/usr/lib64/qt-3.3/include PERL_MB_OPT=--install_base /root/perl5 SSH_TTY=/dev/pts/2 QT_GRAPHICSSYSTEM_CHECKED=1 USER=root LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: MAIL=/var/spool/mail/root PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 CONDA=/home/.galaxy/tooldeps/_conda PWD=/home/.galaxy/tooldeps/_conda/envs LANG=en_ZA.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles LOADEDMODULES= KDEDIRS=/usr PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] SELINUX_LEVEL_REQUESTED= HISTCONTROL=ignoredups SHLVL=1 HOME=/root CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] PERL_LOCAL_LIB_ROOT=:/root/perl5 LOGNAME=root QTLIB=/usr/lib64/qt-3.3/lib SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/0 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins PERL_MM_OPT=INSTALL_BASE=/root/perl5 XAUTHORITY=/tmp/.Xauthority.root BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:38:15 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the help?
Ciao, Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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The integrity and confidentiality of this email is governed by these terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer > Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule <http://www.sun.ac.za/emaildisclaimer >
So those files are "just not there" due to a faulty install? And the repair is to delete the __toolname.x.x.x folders from the _conda/envs folder and force conda to reinstall them? Where can I look for the channel priorities and is there a standard rule for them? Thanks for your input - must appreciated! gerhard ________________________________ From: Björn Grüning <bjoern.gruening@gmail.com> Sent: 10 July 2018 08:49:04 To: Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment Which means that your conda envs are not what they are supposed to be. You can fix this by removing the folder and let Galaxy re-created them, but you should figure out why they are "empty". Maybe a wrong channel priority or network issues during installation? Hope that helps. You could also from insite the env, do a `conda install ...`
Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found
Environment is:
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env XDG_SESSION_ID=45352 HOSTNAME=storage1.hpc SELINUX_ROLE_REQUESTED= TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=10.55.40.3 55438 22 PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5: SELINUX_USE_CURRENT_RANGE= QTDIR=/usr/lib64/qt-3.3 OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0 QTINC=/usr/lib64/qt-3.3/include PERL_MB_OPT=--install_base /root/perl5 SSH_TTY=/dev/pts/2 QT_GRAPHICSSYSTEM_CHECKED=1 USER=root LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: MAIL=/var/spool/mail/root PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 CONDA=/home/.galaxy/tooldeps/_conda PWD=/home/.galaxy/tooldeps/_conda/envs LANG=en_ZA.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles LOADEDMODULES= KDEDIRS=/usr PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] SELINUX_LEVEL_REQUESTED= HISTCONTROL=ignoredups SHLVL=1 HOME=/root CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] PERL_LOCAL_LIB_ROOT=:/root/perl5 LOGNAME=root QTLIB=/usr/lib64/qt-3.3/lib SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/0 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins PERL_MM_OPT=INSTALL_BASE=/root/perl5 XAUTHORITY=/tmp/.Xauthority.root BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:38:15 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the help?
Ciao, Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
So those files are "just not there" due to a faulty install?
Seems so. You can try for hisat as well. The questions is why :(
And the repair is to delete the __toolname.x.x.x folders from the _conda/envs folder and force conda to reinstall them?
Yes.
Where can I look for the channel priorities and is there a standard rule for them?
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L2... Cheers, Bjoern
Thanks for your input - must appreciated!
gerhard
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:49:04 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Which means that your conda envs are not what they are supposed to be.
You can fix this by removing the folder and let Galaxy re-created them, but you should figure out why they are "empty". Maybe a wrong channel priority or network issues during installation?
Hope that helps. You could also from insite the env, do a `conda install ...`
Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found
Environment is:
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env XDG_SESSION_ID=45352 HOSTNAME=storage1.hpc SELINUX_ROLE_REQUESTED= TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=10.55.40.3 55438 22 PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5: SELINUX_USE_CURRENT_RANGE= QTDIR=/usr/lib64/qt-3.3 OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0 QTINC=/usr/lib64/qt-3.3/include PERL_MB_OPT=--install_base /root/perl5 SSH_TTY=/dev/pts/2 QT_GRAPHICSSYSTEM_CHECKED=1 USER=root LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: MAIL=/var/spool/mail/root PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 CONDA=/home/.galaxy/tooldeps/_conda PWD=/home/.galaxy/tooldeps/_conda/envs LANG=en_ZA.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles LOADEDMODULES= KDEDIRS=/usr PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] SELINUX_LEVEL_REQUESTED= HISTCONTROL=ignoredups SHLVL=1 HOME=/root CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] PERL_LOCAL_LIB_ROOT=:/root/perl5 LOGNAME=root QTLIB=/usr/lib64/qt-3.3/lib SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/0 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins PERL_MM_OPT=INSTALL_BASE=/root/perl5 XAUTHORITY=/tmp/.Xauthority.root BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:38:15 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the help?
Ciao, Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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Hi - We have been trying to clean up the Galaxy tool deps ... have this interesting log as a result. Getting a lot of these: "DependencyException: Conda dependency seemingly installed but failed to build job environment." I am curious about the way files play in different locations in Galaxy: For example when tools are installed - Bowtie2, hisat2 or trim-galore ... the same file exists in _conda/pkgs, _conda/envs/__too.xx and _conda/envs/mulled-1-xxx Is something dynamically pathing the executables into environment variables on the fly when a tool is launched? Anyway - here's the interesting log. I think we are going to have to start from the beginning and redo our galaxy. Tx Gerhard galaxy.tools.deps DEBUG 2018-07-11 09:00:44,989 Using dependency bowtie2 version 0d9cd7487cc9 of type galaxy_package galaxy.tools.deps DEBUG 2018-07-11 09:00:45,047 Using dependency samtools version 1.8 of type conda galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:00:45,113 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug list --name __samtools@1.8 --export > '/scratch2/galaxy/tmp/jobdepsE4Lr1n08340d69faa2de38b5657876909fd6669c7f31431857f443b6be50341be135e5/__samtools@1.8' galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:00:59,860 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --unknown --offline --prefix /home/.galaxy/database/jobs_directory/007/7553/conda-env --file /scratch2/galaxy/tmp/jobdepsE4Lr1n08340d69faa2de38b5657876909fd6669c7f31431857f443b6be50341be135e5/__samtools@1.8 Fetching package metadata ... .Solving package specifications: .... UnsatisfiableError: The following specifications were found to be in conflict: - bzip2 1.0.6 3 - krb5 1.13.2 0 Use "conda info <package>" to see the dependencies for each package. galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:01:53,255 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug clean --tarballs -y Cache location: /home/.galaxy/tooldeps/_conda/pkgs Will remove the following tarballs: /home/.galaxy/tooldeps/_conda/pkgs ---------------------------------- r-plogr-0.2.0-r341h6115d3f_0.tar.bz2 17 KB r-getopt-1.20.2-r3.4.1_0.tar.bz2 29 KB libpng-1.6.28-2.tar.bz2 302 KB libtiff-4.0.7-1.tar.bz2 488 KB r-withr-2.1.1-r3.4.1_0.tar.bz2 130 KB r-stringi-1.2.3-r341_0.tar.bz2 704 KB libxml2-2.9.5-1.tar.bz2 5.0 MB r-nlme-3.1_131-r3.4.1_0.tar.bz2 2.2 MB r-rcpparmadillo-0.8.500.0-r3.4.1_0.tar.bz2 1.2 MB r-gtools-3.8.1-r341_0.tar.bz2 265 KB cairo-1.14.6-5.tar.bz2 1.2 MB r-ggplot2-3.0.0-r341h6115d3f_0.tar.bz2 3.0 MB freetype-2.7-2.tar.bz2 2.8 MB r-stringr-1.3.1-r341_0.tar.bz2 164 KB r-rcpp-0.12.16-r3.4.1_0.tar.bz2 3.3 MB r-mgcv-1.8_24-r341_0.tar.bz2 2.4 MB r-rjson-0.2.15-r3.4.1_0.tar.bz2 123 KB --------------------------------------------------- Total: 23.4 MB Removing r-plogr-0.2.0-r341h6115d3f_0.tar.bz2 Removing r-getopt-1.20.2-r3.4.1_0.tar.bz2 Removing libpng-1.6.28-2.tar.bz2 Removing libtiff-4.0.7-1.tar.bz2 Removing r-withr-2.1.1-r3.4.1_0.tar.bz2 Removing r-stringi-1.2.3-r341_0.tar.bz2 Removing libxml2-2.9.5-1.tar.bz2 Removing r-nlme-3.1_131-r3.4.1_0.tar.bz2 Removing r-rcpparmadillo-0.8.500.0-r3.4.1_0.tar.bz2 Removing r-gtools-3.8.1-r341_0.tar.bz2 Removing cairo-1.14.6-5.tar.bz2 Removing r-ggplot2-3.0.0-r341h6115d3f_0.tar.bz2 Removing freetype-2.7-2.tar.bz2 Removing r-stringr-1.3.1-r341_0.tar.bz2 Removing r-rcpp-0.12.16-r3.4.1_0.tar.bz2 Removing r-mgcv-1.8_24-r341_0.tar.bz2 Removing r-rjson-0.2.15-r3.4.1_0.tar.bz2 galaxy.jobs.runners ERROR 2018-07-11 09:01:55,876 (7553) Failure preparing job Traceback (most recent call last): File "/home/.galaxy/lib/galaxy/jobs/runners/__init__.py", line 192, in prepare_job job_wrapper.prepare() File "/home/.galaxy/lib/galaxy/jobs/__init__.py", line 869, in prepare self.dependency_shell_commands = self.tool.build_dependency_shell_commands(job_directory=self.working_directory) File "/home/.galaxy/lib/galaxy/tools/__init__.py", line 1556, in build_dependency_shell_commands tool_instance=self File "/home/.galaxy/lib/galaxy/tools/deps/__init__.py", line 113, in dependency_shell_commands return [dependency.shell_commands() for dependency in ordered_dependencies] File "/home/.galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 469, in shell_commands self.build_environment() File "/home/.galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 464, in build_environment raise DependencyException("Conda dependency seemingly installed but failed to build job environment.") DependencyException: Conda dependency seemingly installed but failed to build job environment. galaxy.jobs DEBUG 2018-07-11 09:01:56,213 fail(): Moved /home/.galaxy/database/jobs_directory/007/7553/galaxy_dataset_19326.dat to /home/.galaxy/database/files/013/dataset_13389.dat ________________________________ From: Björn Grüning <bjoern.gruening@gmail.com> Sent: 10 July 2018 08:56:37 To: Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
So those files are "just not there" due to a faulty install?
Seems so. You can try for hisat as well. The questions is why :(
And the repair is to delete the __toolname.x.x.x folders from the _conda/envs folder and force conda to reinstall them?
Yes.
Where can I look for the channel priorities and is there a standard rule for them?
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L2... Cheers, Bjoern
Thanks for your input - must appreciated!
gerhard
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:49:04 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Which means that your conda envs are not what they are supposed to be.
You can fix this by removing the folder and let Galaxy re-created them, but you should figure out why they are "empty". Maybe a wrong channel priority or network issues during installation?
Hope that helps. You could also from insite the env, do a `conda install ...`
Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found
Environment is:
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env XDG_SESSION_ID=45352 HOSTNAME=storage1.hpc SELINUX_ROLE_REQUESTED= TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=10.55.40.3 55438 22 PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5: SELINUX_USE_CURRENT_RANGE= QTDIR=/usr/lib64/qt-3.3 OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0 QTINC=/usr/lib64/qt-3.3/include PERL_MB_OPT=--install_base /root/perl5 SSH_TTY=/dev/pts/2 QT_GRAPHICSSYSTEM_CHECKED=1 USER=root LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: MAIL=/var/spool/mail/root PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 CONDA=/home/.galaxy/tooldeps/_conda PWD=/home/.galaxy/tooldeps/_conda/envs LANG=en_ZA.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles LOADEDMODULES= KDEDIRS=/usr PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] SELINUX_LEVEL_REQUESTED= HISTCONTROL=ignoredups SHLVL=1 HOME=/root CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] PERL_LOCAL_LIB_ROOT=:/root/perl5 LOGNAME=root QTLIB=/usr/lib64/qt-3.3/lib SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3 LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/0 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins PERL_MM_OPT=INSTALL_BASE=/root/perl5 XAUTHORITY=/tmp/.Xauthority.root BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 10 July 2018 08:38:15 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the help?
Ciao, Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerhardv@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues. But there is still a pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] || MAX_TRIES=3 COUNT=0 while [ $COUNT -lt $MAX_TRIES ]; do . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1 if [ $? -eq 0 ];then break else let COUNT=COUNT+1 if [ $COUNT -eq $MAX_TRIES ];then echo "Failed to activate conda environment! Error was:" cat conda_activate.log exit 1 fi sleep 10s fi done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail; ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found
The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------ *From:* Björn Grüning <bjoern.gruening@gmail.com> *Sent:* 05 July 2018 22:00:58 *To:* Van Wageningen, GERHARD [gerhardv@sun.ac.za]; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda environment Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not the conda version of python.
Have a look at https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers...
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
galaxyproject/galaxy <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample> github.com galaxy - Data intensive science for everyone.
to configure the order of dependency resolution in Galaxy.
Cheers, Bjoern
Hi All
I have recently started learning the Galaxy setup starting with an upgrade. Made some headway but I was wondering if someone could comment on a problem that has emerged. The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage tools.
In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was: Fatal Python error: Py_Initialize: Unable to get the locale encoding File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
Thanks, hopefully someone has seen this before ...
regards, Gerhard
[program:web] command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini directory = /home/.galaxy umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy numprocs = 1 stopsignal = INT
[program:handler] command = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s directory = /home/.galaxy process_name = handler%(process_num)s numprocs = 1 umask = 022 autostart = true autorestart = true startsecs = 10 user = galaxy environment = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/" stdout_logfile = /home/.galaxy/handler%(process_num)s.log redirect_stderr = true
[group:galaxy] programs = handler, web
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participants (2)
-
Björn Grüning -
Van Wageningen, GERHARD [gerhardv＠sun.ac.za]