OK, so I've modified my galaxy.ini to set `preserve_python_environment= legacy` Then I 'm going back to the good shed_tool_conf.xml file : it means no modification in this file regarding the original. I've restarted galaxy and the error traced in https://github.com/galaxyproject/galaxy/issues/4591 reappears. So, I'm answering you in https://github.com/galaxyproject/galaxy/issues/4591 and may be the problem here will disappear.
Thanks again for your help 2017-10-03 10:41 GMT+02:00 Marius van den Beek <[email protected]>: > So the `preserve_python_environment = legacy_and_local` setting is causing > this for you. > Now normally deeptools is not a local tool, but I understand that because of > https://github.com/galaxyproject/galaxy/issues/4591, > you have manipulated the shed_tool_conf.xml file, and it is now being > considered as a local tool. > In any case this setting should be set to legacy_and_local only if you > experience difficulties when it is not set, > that is why `legacy` is the default. > > > On 3 October 2017 at 10:30, julie dubois <[email protected]> wrote: >> >> When I run computeMatrix, I have on ly this in the log file : >> >> 192.168.000.000 - - [03/oct./2017:10:16:07 +0200] "POST >> /galaxy/api/tools/deeptools_compute_matrix/build HTTP/1.1" 200 - >> >> "http://192.168.100.000:8080/galaxy?job_id=7e6a9fe53e29fc38&__identifer=tmmenbexqep"; >> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:37.0) Gecko/20100101 >> Firefox/37.0" >> >> On the job working directory I have this in tool_script.sh : >> #!/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 "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then >> exit 42 >> fi >> export >> PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/[email protected]/bin' >> ; computeMatrix --version > >> /data/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_38413 2>&1; ln -f >> -s "/data/galaxy-dist/database/files/080/dataset_80817.dat" >> "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw" && ln -f -s >> "/data/galaxy-dist/database/files/080/dataset_80593.dat" >> "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed" && >> computeMatrix scale-regions --regionsFileName >> 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed' --scoreFileName >> 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw' --outFileName >> '/data/galaxy-dist/database/files/080/dataset_80995.dat' >> --numberOfProcessors "${GALAXY_SLOTS:-4}" --regionBodyLength 500 >> >> It seems to export the good path for executable. So I don't understand. >> >> In the galaxy_38413.sh : >> #!/bin/bash >> >> >> >> # The following block can be used by the job system >> # to ensure this script is runnable before actually attempting >> # to run it. >> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then >> exit 42 >> fi >> >> GALAXY_SLOTS="1"; export GALAXY_SLOTS; >> export GALAXY_SLOTS >> PRESERVE_GALAXY_ENVIRONMENT="True" >> GALAXY_LIB="/data/galaxy-dist/lib" >> if [ "$GALAXY_LIB" != "None" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; >> then >> if [ -n "$PYTHONPATH" ]; then >> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" >> else >> PYTHONPATH="$GALAXY_LIB" >> fi >> export PYTHONPATH >> fi >> >> GALAXY_VIRTUAL_ENV="/data/galaxy-dist/.venv" >> if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \ >> -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" -a >> "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then >> . "$GALAXY_VIRTUAL_ENV/bin/activate" >> fi >> echo "$GALAXY_SLOTS" > >> >> '/data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_galaxy_slots' >> date +"%s" > >> /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_start >> cd /data/galaxy-dist/database/job_working_directory/038/38413 >> rm -rf working; mkdir -p working; cd working; >> /data/galaxy-dist/database/job_working_directory/038/38413/tool_script.sh; >> return_code=$?; cd >> '/data/galaxy-dist/database/job_working_directory/038/38413'; >> if [ "$GALAXY_LIB" != "None" ]; then >> if [ -n "$PYTHONPATH" ]; then >> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" >> else >> PYTHONPATH="$GALAXY_LIB" >> fi >> export PYTHONPATH >> fi >> if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f >> "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then >> . "$GALAXY_VIRTUAL_ENV/bin/activate" >> fi >> GALAXY_PYTHON=`command -v python` >> export >> PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/[email protected]/bin' >> ; python >> "/data/galaxy-dist/database/job_working_directory/038/38413/set_metadata_c9AkjG.py" >> "/data/galaxy-dist/database/job_working_directory/038/38413/registry.xml" >> >> "/data/galaxy-dist/database/job_working_directory/038/38413/working/galaxy.json" >> >> "/data/galaxy-dist/database/job_working_directory/038/38413/metadata_in_HistoryDatasetAssociation_72822_Eqsgna,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_kwds_HistoryDatasetAssociation_72822_3VQ3be,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_out_HistoryDatasetAssociation_72822_TQg8Pq,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_results_HistoryDatasetAssociation_72822_ctopJa,/data/galaxy-dist/database/files/080/dataset_80995.dat,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_override_HistoryDatasetAssociation_72822_Izp4CZ" >> 5242880; sh -c "exit $return_code" >> echo $? > >> /data/galaxy-dist/database/job_working_directory/038/38413/galaxy_38413.ec >> date +"%s" > >> /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_end >> >> >> May be my galaxy.ini in not well configured for conda. >> For the moment concerning conda in galaxy.ini, I have these lines >> uncommented : >> >> preserve_python_environment = legacy_and_local >> dependency_resolvers_config_file = config/dependency_resolvers_conf.xml >> >> >> >> 2017-10-03 9:53 GMT+02:00 Marius van den Beek <[email protected]>: >> > Also upon re-reading I see that your dependency is being picked up from >> > /usr/local/bin, >> > which indicates that this isn't using conda at all. >> > A small excerpt from the logs when you try to run the tool may be >> > helpful >> > to understand what is going on there. >> > >> > Best, >> > Marius >> > >> > On 3 October 2017 at 09:29, Marius van den Beek <[email protected]> >> > wrote: >> >> >> >> Hi Julie, >> >> >> >> any chance you are setting PYTHONPATH before starting galaxy's job >> >> handlers (a common place would the supervisor config, in case you're >> >> using >> >> that)? >> >> This will interfere with all python modules that are installed via >> >> conda. >> >> >> >> Best, >> >> Marius >> >> >> >> On 3 October 2017 at 09:13, julie dubois <[email protected]> wrote: >> >>> >> >>> Dear Greg, >> >>> I read your discussion with @bgruening and I think it's not exactly >> >>> the same. Because in my case, The executable IS present in my >> >>> galaxy-dist/tool_dependency/_conda/envs/[email protected]/bin . >> >>> The problem is far away in the execution when the tool (computeMatrix >> >>> in my example) try to load the python module deeptools.computeMatrix. >> >>> So is there a solution to discover where is the problem ? >> >>> >> >>> Thanks >> >>> >> >>> 2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <[email protected]>: >> >>> > This looks like the issue I’ve recently seen as well - I just >> >>> > discussed >> >>> > this >> >>> > with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc. I’m >> >>> > using a >> >>> > work-around of creating the __deeptools conda env manually. In my >> >>> > case, I’m >> >>> > not installing the whole suite, just the bamCoverage tool from the >> >>> > TS - >> >>> > >> >>> > >> >>> > https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d. >> >>> > My work-around is to create the conda env manually: >> >>> > >> >>> > $conda create -n [email protected] deep tools=2.5.1 >> >>> > >> >>> > This env is created in the conda environment outside of Galaxy, so I >> >>> > just >> >>> > copy it to the conda environment I’ve configured for Galaxy. This >> >>> > works, >> >>> > but it seems there is some issue with the installation from the TS, >> >>> > so >> >>> > perhaps a more ling term fix is needed. >> >>> > >> >>> > >> >>> > On Oct 2, 2017, at 8:59 AM, julie dubois <[email protected]> wrote: >> >>> > >> >>> > Hi dev team, >> >>> > >> >>> > I have a very big problem since I updated to galaxy 17.05 with >> >>> > deeptools from toolshed. >> >>> > >> >>> > Due to a bug in galaxy 17.05 with toolshed installed tools (reported >> >>> > in this issue https://github.com/galaxyproject/galaxy/issues/4591), >> >>> > I >> >>> > re-installed deeptools to try to resolve it. >> >>> > Not resolved really but it's another problem. I temporarly bypassed >> >>> > it. >> >>> > >> >>> > Here is my problem : I've installed deeptools from toolshed and when >> >>> > we try to use "compute matrix" for example, we have this error >> >>> > message >> >>> > : >> >>> > >> >>> > Fatal error: Exit code 1 () >> >>> > Traceback (most recent call last): >> >>> > File "/usr/local/bin/computeMatrix", line 4, in <module> >> >>> > from deeptools.computeMatrix import main >> >>> > ImportError: No module named deeptools.computeMatrix >> >>> > >> >>> > It seems that wrapper are installed but not the tool "deeptools". >> >>> > >> >>> > For more information, here it's the way for the installation : >> >>> > search and install via toolshed >> >>> > Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a) >> >>> > Info in Manage tool dependencies : version=2.5.1, resolver=Conda, >> >>> > green check symbol in the line with a list of all deeptools. >> >>> > >> >>> > Galaxy 17.05, commit cfabe37 (21 sept 2017) >> >>> > >> >>> > I've tried to uninstall/reinstall dependencies with conda but >> >>> > without >> >>> > success. >> >>> > >> >>> > Have you any idea to install the deeptools please ? >> >>> > >> >>> > Thanks. >> >>> > Julie >> >>> > ___________________________________________________________ >> >>> > 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/ >> >>> > >> >>> > >> >>> ___________________________________________________________ >> >>> 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/ >> >> >> >> >> > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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