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_conf.xml.sample
>
> <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 >
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>> <http://www.sun.ac.za/emaildisclaimer >
>>
>>
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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 >

The integrity and confidentiality of this email is governed by these terms. Disclaimer
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