April 2014 - galaxy-dev - lists.galaxyproject.org

Package/Module RPY
by Hayes, Curt 08 Apr '14

08 Apr '14

Hi there all, I have searched previous posts, nothing since 2010. I have a local install (production config - postgres, etc - on CENTOS 6.5). Does anyone have RPY working? I install via toolshed and the folder is empty, and shows missing dependencies. >From Galaxy User: Dataset generation errors Dataset 81: Build base quality distribution on data 9 Tool execution generated the following error message: Traceback (most recent call last): File "/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py", line 12, in <module> from rpy import * ImportError: No module named rpy I have attempted to download/install the scripts but they fail with multiple errors (most posts out there have a bad URL) - http://getgalaxyp.org/install.html says use: curl http://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz if you view that it redirects you to another URL. Via shell: R is installed: R version 2.13.0 (2011-04-13) Can someone provide me some help please to get it working via Galaxy? I understand it works in Central. >From Toolshed: Name Version Type Installation status rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_reposito…> 1.0.3 package Error Toolshed Error: In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: Python.h: No such file or directory In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2110.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: error: #error Must use Python with unicode enabled. <truncated> Thanks, Curt CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

3 7

Check file before uploading
by Neil.Burdett＠csiro.au 08 Apr '14

08 Apr '14

Hi When selecting a file or after clicking on "Execute" to upload a file is it possible to check the file is appropriate i.e. by checking file extension etc, before the file is actually uploaded and put into the database? So the user can't upload the wrong file/format Thanks Neil Neil Burdett Software Engineer | The Australian e-Health Research Centre Computational Informatics CSIRO E: Neil.Burdett(a)csiro.au T: 07 3253 3626 Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029 www.csiro.au | http://milxview.csiro.au

2 1

Installing S-Mart on Mac SOX local instance
by Bernardo Bello 08 Apr '14

08 Apr '14

Hi, I am having problems to install a tool from tool shed named S_MART on my local Galaxy. The reason to install S_MART is to use DETR'PROK in Galaxy. Attached is the 'error' Galaxy indicates after installing some programs from toolshed. I've seen this related post, but I don't know if we are talking about the same problem.<http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td46…> Here are the commands aI've used up to now: Thanks hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable sh run.sh # gave errors, so see below # solve problem at startup ( https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html) % export LC_ALL='en_US.UTF-8' % sh run.sh done # Go to http://localhost:8080/ and register as popnard(a)gmail.com # Setup admin user (https://wiki.galaxyproject.org/Admin/Interface) To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. admin_users = popnard(a)gmail.com # Set 'Tool Dependencies' https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&re… mkdir tool_dependency_dir done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of universe_wsgi.ini to a path writable by the Galaxy server. done # restart server First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. # http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-shed-… # Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox> done # INSTALL R done # ADD R PACKAGES R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}' R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}' -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *

1 0

krona to metaphlan patch
by Langhorst, Brad 08 Apr '14

08 Apr '14

I’m running with these local additions to Dannon’s metaphlan repo. I think it would be better to add these to the current metaphlan repo than to release them standalone.

2 1

extract_genomic_dna.py
by Adhemar 08 Apr '14

08 Apr '14

Hi, In order to have the transcript_id for each sequence extracted from the cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding the following lines after line 153: attributes = gff_util.parse_gff_attributes( feature[8] ) if ( "transcript_id" in attributes ): name = attributes.get( "transcript_id", None ) This way the variable name gets the transcript_id if it exists. If it's correct, I would appreciate this modification in future galaxy distributions. Thanks! Adhemar

2 1

Problem with executing newly installed tools (via admin)
by Nicolas Cybulski 08 Apr '14

08 Apr '14

Ok, a small update on this problem. I have set up a local tool shed with in it a repository that holds 2 tool definitions of the same tool but with different verision nbrs <tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="1.0"> <description>Dummy Tool</description> <command interpreter="python"> dummyTool.py $inputFile $operand $outputFile </command> <inputs> <param name="inputFile" type="data" format="txt" label="Input txt file" /> <param name="operand" type="text" size="2" label="Operand"/> </inputs> <outputs>  <data name="outputFile" format="txt" label="${tool.name}: output" /> </outputs> <tests> <test> <param name="inputFile" value="dummyTool_input.txt" ftype="txt"/> <param name="operand" value="2"/> <output name="outputFile" file="dummyTool_output.txt"/> </test> </tests> and: <tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="2.0"> <description>Dummy Tool v2</description> <command interpreter="python"> dummyTool_v2.py $inputFile $operand $outputFile </command> <inputs> <param name="inputFile" type="data" format="txt" label="Input txt file" /> <param name="operand" type="text" size="2" label="Operand"/> </inputs> <outputs>  <data name="outputFile" format="txt" label="${tool.name}: output" /> </outputs> <tests> <test> <param name="inputFile" value="dummyTool_input.txt" ftype="txt"/> <param name="operand" value="2"/> <output name="outputFile" file="dummyTool_output_v2.txt"/> </test> </tests> </tool> </tool> I am successful in installing these tools in Galaxy using out own toolshed. I get the following lines in shed_tool_conf.xml <section id="nicyb_test_3" name="nicyb test 3" version=""> <tool file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper.xml" guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0"> <tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed> <repository_name>testbla2</repository_name> <repository_owner>nicyb</repository_owner> <installed_changeset_revision>4c7117d7f90d</installed_changeset_revision> <id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0</id> <version>1.0</version> </tool> <tool file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper_v2.xml" guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0"> <tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed> <repository_name>testbla2</repository_name> <repository_owner>nicyb</repository_owner> <installed_changeset_revision>4c7117d7f90d</installed_changeset_revision> <id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0</id> <version>2.0</version> </tool> </section> When I look in the tool panel I can see both tools under section nicyb test3. Upon selecting one I get Nicyb Dummy Tool and then a drop down with "version 1.0" and "version 2.0" However, when I change the version nbrs I get the following error: Module MySQLdb.connections:36 in defaulterrorhandler view OperationalError: (OperationalError) (1241, 'Operand should contain 1 column(s)') 'INSERT INTO event (create_time, update_time, history_id, user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, %s)' (datetime.datetime(2014, 4, 8, 14, 34, 48, 567645), datetime.datetime(2014, 4, 8, 14, 34, 48, 567654), 1L, 1L, "Tool params: {'operand': u'', 'tool_state': u'800255db313334303737356537316139353463626339613333356235633261356166623236313166623137643a3762323236663730363537323631366536343232336132303232356332323465366636653635356332323232326332303232356635663730363136373635356635663232336132303330326332303232356635663732363537323735366535663732363536643631373035663661366636323566363936343566356632323361323036653735366336633263323032323639366537303735373434363639366336353232336132303232333233323232376471002e', 'refresh': u'refresh', 'inputFile': u'22'}", 16L, [u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0', u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0']) Is there anyone with similar experiences or an explanation for this ? Kind regards, Nicolas On 04/02/2014 06:00 PM, galaxy-dev-request(a)lists.bx.psu.edu wrote: > Subject: > [galaxy-dev] Problem with executing newly installed tools (via admin) > From: > "Nicolas Cybulski" <nicyb(a)psb.vib-ugent.be> > Date: > 04/02/2014 10:38 AM > > To: > galaxy-dev(a)lists.bx.psu.edu > > > Hi, > > I have installed the Picard tools using the Tool-shed functionality in > the admin tools. > The tools and requisites have been correctly installed and run correctly. > The insert statement to the event table fails however. I get the > following error on screen: > > |OperationalError: (OperationalError) (1241, 'Operand should contain 1 > column(s)') 'INSERT INTO event (create_time, update_time, history_id, > user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, > %s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142), > datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool > params: {'histWidth': u'0', 'deviations': u'10.0', 'malevel': > u'ALL_READS', 'input_file': u'5266', 'out_prefix': u'Insertion size > metrics', 'refresh': u'refresh', 'minPct': u'0.05', 'tool_state': > u'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343", > 1468L, > [u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', > u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']) > > |The problem seems to be a duplicate entry of the tool_id > > |[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', > u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'] > > |In the shed_tool_conf.xml the tools are generated as follows > > <tool > file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardIns…"guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0"> > > If I change this guid to something less complicated like > > <tool > file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardIns…" > guid="testPicard"> > > and restart galaxy it works ... > for all tools (so not only the one that I've changed). > > Does anyone have an idea as to why this is ? > > kind regards, > > Nicolas

1 0

patches to bjorn's bismark wrapper
by Langhorst, Brad 08 Apr '14

08 Apr '14

This patch updates bjorn’s bismark wrapper to work with latest bismark and allows methylation extraction from SAM or BAM files. It no longer sorts the BAM from bismark (to allow methylation extraction to work).

2 1

Securing REMOTE_USER against local users
by Eric Rasche 07 Apr '14

07 Apr '14

1 0

authorize non admin user to only link a directory of files
by Berner, Thomas 07 Apr '14

07 Apr '14

Hi, we recently activated the feature for non admin users which allows them to upload a directory of files: ... # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. #user_library_import_dir = None user_library_import_dir = /opt/galaxy/galaxy-share/ ... However we would like to restrict the permission to only link to their files without copying them into galaxy, is this possible? Greetings, Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner(a)jki.bund.de

2 2

Data manager for the BLAST database *.loc files?
by Peter Cock 07 Apr '14

07 Apr '14

Hi Daniel, Would you be OK with me/us incorporating your example Galaxy Data Manager [1] for NCBI BLAST databases http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_bla… into the Galaxy BLAST wrappers repository https://github.com/peterjc/galaxy_blast/ under the MIT licence, and then extending it? If you have a GitHub account I can do that as a commit with you as the author to make the attribution explicit. See also https://github.com/peterjc/galaxy_blast/issues/22 where we're discussing this issue. Thanks, Peter [1] This is described in Daniel's new paper, Blankenberg et al (2014) Wrangling Galaxy's reference data http://dx.doi.org/10.1093/bioinformatics/btu119 and the Galaxy wiki: https://wiki.galaxyproject.org/Admin/Tools/DataManagers

2 2