Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/[email protected]) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version -bash: trim_galore: command not found Environment is: (/home/.galaxy/tooldeps/_conda/envs/[email protected]) [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/[email protected] 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/[email protected]/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/[email protected] 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/[email protected]) \[\e[1;31;40m\][\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/[email protected] 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 $*` } _=/usr/bin/env (/home/.galaxy/tooldeps/_conda/envs/[email protected]) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ ________________________________ From: Björn Grüning <[email protected]> Sent: 10 July 2018 08:38:15 To: Van Wageningen, GERHARD [[email protected]]; [email protected] 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/[email protected] 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 [[email protected]]: > 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/[email protected]" ] || > MAX_TRIES=3 > COUNT=0 > while [ $COUNT -lt $MAX_TRIES ]; do > . /home/.galaxy/tooldeps/_conda/bin/activate > '/home/.galaxy/tooldeps/_conda/envs/[email protected]' > > 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 <[email protected]>; > [email protected] > > ------------------------------------------------------------------------ > *From:* Björn Grüning <[email protected]> > *Sent:* 05 July 2018 22:00:58 > *To:* Van Wageningen, GERHARD [[email protected]]; > [email protected] > *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 > >> >> >> ___________________________________________________________ >> 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/ >> > <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. 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