galaxy-dev December 2015

galaxy-dev@lists.galaxyproject.org

41 participants
59 discussions

bx-python issue with intersect and subtract tools
by Poole, Richard 12 Feb '16

12 Feb '16

Hi all, I just used the subtract tool (installed under Operate on Genomic Intervals) on my own Galaxy server for the first time in a very long time and got this error message from the tool: Traceback (most recent call last): File "/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py<http://toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/…>", line 16, in <module> from bx.intervals.io import GenomicInterval, NiceReaderWrapper ImportError: No module named bx.intervals.io So I uninstalled the intersect and subtract tools, plus the bx-python 0.7.1 package plus the galaxy-ops package and reinstalled both tools from the toolshed using the latest revisions of each from devteam. I now get this error message: /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module bx was already imported from /Users/galaxy/galaxy-dist/tool-dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.7/site-packages/bx/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path self.check_version_conflict() Traceback (most recent call last): File "/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py<http://toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/…>", line 21, in <module> from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff ImportError: No module named utils.gff_util Does this suggest an incompatibility somehow with the the egg which is installed at startup and is versions 0.7.2 - I tried manually editing the egg file but could not switch that to 0.7.1 I also then tried updating Galaxy to latest release 15.07 and even 15.10 which appeared in the git tag list as I writing this email, but no fix there - my Galaxy is running on a Mac OS X 10.10.5 Yosemite. Any thoughts on how to resolve this problem? Cheers, Rich Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 518 Rockefeller 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

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Upload issue in local installation
by Batsal Devkota 05 Feb '16

05 Feb '16

I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever. In the terminal window where I start galaxy, I get the following error report: 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" The last line keeps going for ever... writes new line every 4 secs. I am stuck and don't know where to look. Please help. Batsal.

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REST API - Tool input information
by Koehorst, Jasper 01 Feb '16

01 Feb '16

Is it possible to get tool input information through the REST api? For example, I would like to know for a specific tool to retrieve the inputs needed and the types of inputs being either integer, dataset, string, etc… Kind regards, Jasper Koehorst

2 1

'bp_genbank2gff3' installation error and running error
by Wang, Xiaofei 28 Jan '16

28 Jan '16

Dear there, I'd like to convert genebank flat file to GFF. So, I am trying to install this tool shed [cid:2d047a8e-cfc4-4e3e-97b4-5225f8dde128] to my local galaxy. But I got an error as below. Does it associated with dependencies? I see it needs these ? [cid:51e76e29-daa7-4f92-a9a8-3687d969f3e6] . How can I check if I have all these? ?[cid:53e1eb6a-f27d-471c-8122-0d575a63c4f2] Also, I see there is the same tool in this website https://galaxy.cbio.mskcc.org/root?tool_id=fml_gbk2gff (see below). It should be also galaxy but I need to register an account for it. Do you know what is the relationship between this website and the galaxy? BTW, I received an error when I used the tool on this website. I think if they are same tool, the galaxy team should know the reason for it. Here is the error as below. GFF Toolkit (v0.1) GROOMING PROGRAMS Examine_GFF<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_examine> file Parent-Child relations FeatureScan<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_available_limits> gives an overview about GFF feature content CONVERTER PROGRAMS GTF_to_GFF3<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gtf2gff3> converter BED_to_GFF3<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_bed2gff> converter GFF3_to_BED<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed> converter GBK-to-GFF<https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gbk2gff> converter ?[cid:56985bc0-77c2-4719-b0f9-d4b36aeb03c0] Thanks! Best, Xiaofei

2 2

python_mysqldb caused zip_safe flag not set
by Mic 19 Jan '16

19 Jan '16

Hello, I tried to install CEAS from testtoolshed, but I have recieved the below error from python_mysqldb (tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f) The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error. I installed MariaDB 10.1 on Ubuntu 14.04 in the following way: apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 0xcbcb082a1bb943db add-apt-repository 'deb [arch=amd64,i386] http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main' apt-get update apt-get install mariadb-server libmariadbclient-dev The INSTALLATION.log shows the following information: ... byte-compiling build/bdist.linux-x86_64/egg/MySQLdb/cursors.py to cursors.pyc creating stub loader for _mysql.so byte-compiling build/bdist.linux-x86_64/egg/_mysql.py to _mysql.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating dist removing 'build/bdist.linux-x86_64/egg' (and everything under it) Creating /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/site.py Processing MySQL_python-1.2.5-py2.7-linux-x86_64.egg Copying MySQL_python-1.2.5-py2.7-linux-x86_64.egg to /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python Adding MySQL-python 1.2.5 to easy-install.pth file Installed /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/MySQL_python-1.2.5-py2.7-linux-x86_64.egg Processing dependencies for MySQL-python==1.2.5 Finished processing dependencies for MySQL-python==1.2.5 ############################################# ############################################# export PYTHONPATH=$PYTHONPATH:/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python && python setup.py install --install-lib /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python --install-scripts /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/bin STDERR zip_safe flag not set; analyzing archive contents... What did I miss? Thank you in advance. Mic

2 1

Please terminate iGeneMap cluster
by Laura Song 12 Jan '16

12 Jan '16

Hi, I accidentally launched iGeneMap cluster. Please help me terminate it. Thanks. Laura

2 1

running in job_working_directory
by Jorrit Boekel 11 Jan '16

11 Jan '16

Dear all, I (finally) started transitioning our lab’s tools from using parallelism (the multi-splitter) towards collections. In the parallelism scenario, tools were run in their respective working dir, resulting from a chdir performed in extract_parts.sh. That was nice. But I see when using collections that there is a workdir around, but the tool is not actually run in it. I often need to symlink to change input file extensions and can’t imagine noone else does that, so I wondered if I was missing something. If I’m not, then here’s my two questions: - Is there an accepted place to symlink files in (and how do I pass the working dir in a tool XML)? I don’t want them in the files/ dir, looks bad, they’re not cleaned, etc etc. - Would it be a bad idea to make tools run inside a workdir, apart from possibly breaking backwards compatibility? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

1 1

Extract features : error loading field data in usegalaxy
by Gildas Le Corguillé 08 Jan '16

08 Jan '16

Hi, One of my user wanted to import a workflow using the tool "Extract features" provided in the galaxy distrib : tools/filters/gff/extract_GFF_Features.xml On my instance, in the workflow canevas, I get this in red "error loading field data" On usegalaxy.org, I happy to observe that it's the same ... Sorry :) Any idea ? Gildas -- ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science) Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr ------------------------------------------------------------------

1 1

This job is waiting to run - Issue after Update to 15.10
by Matthias Enders 04 Jan '16

04 Jan '16

After some trying a college figured out, the Tools are working just fine, but all old datasets are not accessible by the tools via "redo the job". But I can Download them and so on.

2 1

how to access current user's apikey
by rbrown1422＠comcast.net 04 Jan '16

04 Jan '16

Good morning team, Is there a way to access the current user's API Key similar to seeing their email address via a tool's xml parameter "$__user_email__" ? Thanks, Bob

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galaxy-dev December 2015