- galaxy-dev - lists.galaxyproject.org

automatically adding fasta files to "built-in" databases and selecting files questions
by Nikhil Joshi 09 Apr '14

09 Apr '14

Hi all, We have a local install of Galaxy that we use for testing for our bioinformatics courses. I am creating some new tool interfaces for the install. I want to create a tool that will allow a user to automatically add a fasta database to the "built-in" databases (without needing to reboot the server). Is this possible? Along with that issue is that the number of databases for this tool can number in the thousands. Is there a way to easily search the built-in databases for the database you are looking for, and then use that database in a tool? Right now, it is an enormous drop down list which is really annoying and unwieldy. Finally, these tools can take multiple input files, but I really don't like the way galaxy handles that where you have to continually click on "Add another file". Is there a method or work-around in galaxy where you can have a multi-file select? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

2 1

visualization button
by Philippe Moncuquet 09 Apr '14

09 Apr '14

Hi, I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ? Regards, Philip

2 5

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