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_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 >
>>> 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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>>> Please keep all replies on the list by using "reply all"
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>>>    http://galaxyproject.org/search/
>>>
>> <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 >
> <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 >

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule