galaxy-dev October 2016

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Job_id in a galaxy tool
by Katherine Beaulieu 31 Oct '16

31 Oct '16

Hello Galaxy Community, Is it possible to get the job_id listed on the info 'eye' page within a tool wrapper? Katherine

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galaxy - velvet devteam revision 08256557922f
by Fernandez Edgar 31 Oct '16

31 Oct '16

Hey Guys, I need your help understanding what’s happening with velvet devteam revision 08256557922f. After installing it, velvet was giving me the following error: galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness I realized velvet needed that galaxy was restarted. Now, velvet finishes his jobs (becomes green) however, the following message is on galaxy’s Job output not returned from cluster And you can see in the logs of the handler: galaxy.jobs DEBUG 2016-10-31 10:17:08,548 (1669) Working directory for job is: /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669 galaxy.jobs.handler DEBUG 2016-10-31 10:17:08,567 (1669) Dispatching to drmaa runner galaxy.jobs DEBUG 2016-10-31 10:17:08,621 (1669) Persisting job destination (destination id: torque) galaxy.jobs.runners DEBUG 2016-10-31 10:17:08,630 Job [1669] queued (63.397 ms) galaxy.jobs.handler INFO 2016-10-31 10:17:08,652 (1669) Job dispatched galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Building dependency shell command for dependency 'velvet' galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Find dependency velvet version 1.2.10 galaxy.tools.deps DEBUG 2016-10-31 10:17:08,896 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7f80f807bd50> (isnull? False) galaxy.jobs.command_factory INFO 2016-10-31 10:17:08,945 Built script [/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh] for tool command[PACKAGE_BASE=/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f; export PACKAGE_BASE; . /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f/env.sh; velveth 2>&1 | grep "Version" | sed -e 's/Version //' > /home/galaxy/galaxy-prod/database/tmp/GALAXY_VERSION_STRING_1669 2>&1; python /home/galaxy/galaxy-prod/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/velvet/08256557922f/velvet/velveth_wrapper.py '/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat' '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/dataset_4306_files' 21 -fasta -short /home/galaxy/galaxy-prod/database/files/003/dataset_3537.dat] galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True) galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True) galaxy.tools.deps WARNING 2016-10-31 10:17:09,145 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners DEBUG 2016-10-31 10:17:09,153 (1669) command is: mkdir -p working; cd working; /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh; return_code=$?; cd '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669'; python "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/set_metadata_KQTExg.py" "/home/galaxy/galaxy-prod/database/tmp/tmpLU0HQy" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/working/galaxy.json" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_in_HistoryDatasetAssociation_4437_kIYXWa,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_kwds_HistoryDatasetAssociation_4437_ArCXyb,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_out_HistoryDatasetAssociation_4437_l28qWr,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_results_HistoryDatasetAssociation_4437_oTDjOd,/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_override_HistoryDatasetAssociation_4437_8VzdJw" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,202 (1669) submitting file /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.sh galaxy.jobs.runners.drmaa INFO 2016-10-31 10:17:09,210 (1669) queued as 1573.esilbac3a.esi.umontreal.ca galaxy.jobs DEBUG 2016-10-31 10:17:09,214 (1669) Persisting job destination (destination id: torque) galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,642 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:14,848 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job finished normally galaxy.jobs.runners ERROR 2016-10-31 10:17:24,906 (1669/1573.esilbac3a.esi.umontreal.ca) Job output not returned from cluster: [Errno 2] No such file or directory: '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.o' galaxy.model.metadata DEBUG 2016-10-31 10:17:25,314 loading metadata from file for: HistoryDatasetAssociation 4437 galaxy.jobs INFO 2016-10-31 10:17:25,541 Collecting metrics for Job 1669 galaxy.jobs DEBUG 2016-10-31 10:17:25,554 job 1669 ended (finish() executed in (636.363 ms)) galaxy.model.metadata DEBUG 2016-10-31 10:17:25,560 Cleaning up external metadata files Do you have an idea why I’m getting this problem? Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568

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Local galaxy samtools HISAT 2 issue
by evan clark 31 Oct '16

31 Oct '16

I am setting up a production galaxy server and am having an issue with running HISAT 2. It appears that it is not able to find samtools and renders an error within galaxy. Below is the error that it produces. I am unsure how to get the full error log for HISAT. |Traceback(most recent call last): File"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 609,in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code) File"/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1265,in finish dataset.datatype.set_meta( dataset, overwrite=False) File"/home/eclark28/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 347,in set_meta exit_code= subprocess.call( args=command, stderr=open( stderr_name,'wb' ) ) File"/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 523,in call return Popen(*popenargs, **kwargs).wait() File"/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 711,in __init__ errread, errwrite) File"/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 1343,in _execute_child raise child_exception OSError:[Errno 2] No suchfile or directory|

2 1

galaxy venv problem
by Beginner TI 31 Oct '16

31 Oct '16

Hi, During the installation or galaxy instance, I set up a directory to install all the python dependencies. Basically, whenever I install python modules, I do something like: python setup.py install --prefix=/my/python/dir as a result, there are tons of stuff installed there. I added this path to PYTHONPATH. The reason I do this is that I don't want to use sudo to install galaxy python modules. Now the problem...I was hoping not to use virtual env. However galaxy is set to use it's own venv, and during the course of starting, it will unset the PYTHONPATH. That caused that installed tools didn't work because it could not find the modules installed. Here is one example of how it is not working. The tool generated the following command in the script: gca -b /media/libraryfiles/galaxy-data-store/database/files/000/dataset_44.dat --span=3000 -g /media/libraryfiles/dep/cistrome-static-lib/ceaslib/GeneTable/mm9 --name=gca_out >& /media/libraryfiles/galaxy-data-store/database/files/000/dataset_95.dat cp gca_out.xls /media/libraryfiles/galaxy-data-store/database/files/000/dataset_94.dat I could run that command in the terminal successfully, but not in the galaxy. It keeps reporting error that gca_out.xls isn't there. With the PYTHONPATH unset, when I run that command, I would get: Traceback (most recent call last): File "/media/libraryfiles/dep/python/bin/gca", line 32, in <module> import CEAS.inout as inout ImportError: No module named CEAS.inout Once I put the PYTHONPATH back, export PYTHONPATH=/media/libraryfiles/dep/python/lib/python2.7/site-packages then that gca command would generate the correct output file. I tried to use sh run.sh --skip-venv However, it keeps giving me errors. It seems those were from not able to install the dependencies listed in requirements.txt. I then installed those dependencies to my python directory as well. During the course had to remove some that came with system, and install the newer ones. Now it seems to be working. I'm just wondering, is this a good way to using system python with all the dependencies I installed? Thanks, Rui

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Call for GMOD talks at PAG
by Scott Cain 28 Oct '16

28 Oct '16

Hi, I am pleased to announce a call for talks to be given at the Plant and Animal Genomes conference this January in the GMOD workshop on Wednesday, January 18th. Any talks that involve the development or use of GMOD software are welcome. In particular this year, I'd really like to highlight plugins for the various GMOD software packages that support them, like JBrowse, Galaxy and Tripal (of course, Galaxy and Tripal have their own sessions, so you should consider submitting to them too). Please get an abstract, brief summary or a vague title to me as soon as possible so I can start getting it put together. Also, if you'd like to be a co-organizer, please let me drop me a line about that too. I might be able to get you some meeting-related niceties for not very much work. For more information about PAG, see: http://www.intlpag.org Thanks and I look forward to seeing in January, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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odose
by Vos, Michiel 28 Oct '16

28 Oct '16

Dear Galaxy developers, We hereby want to ask if anyone is interested in helping out to repair and update our Galaxy tool 'odose': Webserver<http://www.odose.nl/> Publication<http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062447> Public server page<https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE> Github<https://github.com/ODoSE/galaxy> Odose enables users to perform an array of population genetics tests on prokaryote genomes. Our tool is currently linked to NCBI to download various files, but continuous restructuring at NCBI has resulted in broken links which prevent the pipeline from working. Developer Tim te Beek has moved on outside academia and does not have the time to fix it, but is available to give answer question/give instructions. We believe our tool is highly useful for microbiologists and would greatly appreciate any help from the Galaxy community to get it working properly again! Please get in touch if you would like to know more. Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek Michiel Vos European Centre for Environment and Human Health University of Exeter ESI Building, Penryn Campus TR10 9FE Penryn, UK 0044 (0)1326259464 https://coastalpathogens.wordpress.com/

3 2

Usegalaxy.org Data Rsync Connection refused
by Georgios Nikolis 28 Oct '16

28 Oct '16

1 0

Cannot start Galaxy DistributionNotFound: Paste
by Hernán Piqueras 27 Oct '16

27 Oct '16

Guys I am running CentOS 6.8 in a virtualenv and no matter what, I always get pkg_resources.DistributionNotFound: Paste These were the commands to install and launch Galaxy hg clone https://bitbucket.org/galaxy/galaxy-dist wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py /usr/local/bin/python2.7 virtualenv.py --no-site-packages galaxy_env . ./galaxy_env/bin/activate source ~/galaxy_env/bin/activate sh galaxy-dist/run.sh and even tried to start with some workarounds found in the web (in no particular order): cd /home/galaxy/galaxy-dist && ./scripts/common_startup.sh ./scripts/common_startup.sh --skip-venv --dev-wheels sh galaxy-dist/run.sh --skip-venv --dev-wheels sh galaxy-dist/run.sh --skip-venv sh galaxy-dist/run.sh --replace-pip easy_install paste Also install or upgrade doesn't solve the problem: (galaxy_env)bash-4.1$ pip install paste Requirement already satisfied (use --upgrade to upgrade): paste in ./galaxy_env/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): six in ./galaxy_env/lib/python2.7/site-packages (from paste) (galaxy_env)bash-4.1$ pip install paste --upgrade /home/galaxy/galaxy_env/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/galaxy/galaxy_env/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Collecting paste Using cached Paste-2.0.3-py2-none-any.whl Collecting six>=1.4.0 (from paste) Using cached six-1.10.0-py2.py3-none-any.whl Installing collected packages: six, paste Found existing installation: six 1.9.0 Uninstalling six-1.9.0: Successfully uninstalled six-1.9.0 Found existing installation: Paste 2.0.2 Uninstalling Paste-2.0.2: Successfully uninstalled Paste-2.0.2 Successfully installed paste-2.0.3 six-1.10.0 Using common_startup.sh also doesn't solve the problem: (galaxy_env)bash-4.1$ cd /home/galaxy/galaxy-dist && ./scripts/common_startup.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple /home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in ./.venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) You are using pip version 8.0.2+gx2, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Requirement already satisfied (use --upgrade to upgrade): MySQL-python in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) You are using pip version 8.0.2+gx2, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. (galaxy_env)bash-4.1$ ./galaxy-dist/scripts/common_startup.sh --skip-venv Could not open requirements file: [Errno 2] No such file or directory: 'requirements.txt' This is the complete log (with normal startup): (galaxy_env)bash-4.1$ sh galaxy-dist/run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple /home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in ./.venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) You are using pip version 8.0.2+gx2, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Requirement already satisfied (use --upgrade to upgrade): MySQL-python in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) You are using pip version 8.0.2+gx2, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Activating virtualenv at .venv Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 637, in command server = loadserver(server_spec, name=server_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 303, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 502, in get_context section) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 524, in _context_from_use object_type, name=use, global_conf=global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 454, in get_context global_conf=global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 376, in _loadegg return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 668, in get_context object_type, name=name) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 688, in find_egg_entry_point pkg_resources.require(self.spec) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 666, in require File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 565, in resolve pkg_resources.DistributionNotFound: Paste Any hints?

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New Galaxy Arabic Community
by Dave Clements 27 Oct '16

27 Oct '16

Hello all, أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام أي شخص مهتم بالجلاكسي بلاتفورم جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول على نفس النتائج عند إجراء التحليل مرات عديدة. السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل المعلومات الحيوية النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز جالاكسي عن العديد من الأدوات الاخرى الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر أيضا . جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك واستخدامها ------------------------------ We are pleased to announce the launch of the *Galaxy Arabic community <https://wiki.galaxyproject.org/Community/Arabic>.* Galaxy Arabic supports and promotes Galaxy activity for the Arabic speaking community and in Arabic speaking regions of the world. If you are interested in joining the community, please - Follow @Galaxy_Arabic on Twitter <http://twitter.com/galaxy_arabic> - Join the Galaxy Arabic mailing list <https://lists.galaxyproject.org/listinfo/galaxy-arabic>. Regional Galaxy news will be posted here, and you can also ask fellow Arabic speakers support questions. - Join the Galaxy Arabic Facebook group <http://bit.ly/2ek7fTh> We look forward to connecting and growing the Arabic speaking Galaxy community. Thanks, Abdelazeem Abdelhameed <abdelazeem_abdelhameed2015505(a)yahoo.com> and Dave Clements <https://wiki.galaxyproject.org/DaveClements> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

2 1

Tool wrapper NotFound error
by evan clark 27 Oct '16

27 Oct '16

I have written the below tool wrapper and when running in galaxy I receive the error. I am not sure the issue with the wrapper. ~~~~ Traceback (most recent call last): File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 897, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/tools/evaluation.py", line 445, in build raise e NotFound: cannot find 'library' ~~~~ ~~~~ <tool id="miso" name="Miso" version="1.0.0"> <description>Alternative splicing analysis</description> <version_command>python /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py --version </version_command> <command> <![CDATA[ mkdir -p '${output.files_path}/indexed_gff' && mkdir -p '${output.files_path}/exonUtil' && mkdir -p '${output.files_path}/pe' && mkdir -p '${output.files_path}/miso' && ~/galaxy_production/python/bin/index_gff --index '${input_gff}' '${output.files_path}/indexed_gff' #if str( $library.type ) == "paired": && /home/eclark28/galaxy_production/python/bin/exon_utils --get-const-exons '${master_input_gff}' --min-exon-size '${exon_size}' --output-dir '${output.files_path}/exonUtil' && ~/galaxy_production/python/bin/pe_utils --compute-insert-len '${bam_file}' '${output.files_path}/exonUtil/${master_input_gff}.min_${exon_size}.const_exons.gff' --output-dir '${output.files_path}/pe' #end if && python /home/eclark28/galaxy_production/python/lib/python2.7/site-packages/misopy/miso.py --run '${output.files_path}/indexed_gff' '${bam_file}' --output-dir '${output.files_path}/miso' --read-len '${read_length}' #if str( $library.type ) == "paired": --paired-ended `'${output.files_path}/pe/insert-dist/${master_input_gff}.insert_len' | parseExonUtil.pl` #end if --use-cluster && tree -H ./ ${output} ]]> </command> <inputs> <section name="basicOptions" title="Basic Options" expanded="True">  <param name="bam_file" type="data" label="BAM File" /> <param name="input_gff" type="data" label="Input GFF" /> <param name="exon_size" type="integer" label="Exon Size" value="1000" /> <param name="read_length" type="integer" label="Read Length" value="99" /> <conditional name="library"> <param name="type" type="select" label="Is this single or paired library"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> </param> <when value="paired"> <param name="master_input_gff" type="data" label="Master GFF" /> </when> <when value="single"> </when> </conditional> </section> </inputs> <outputs> <data format="html" name="output" /> </outputs> </tool> ~~~~

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galaxy-dev October 2016