galaxy-dev August 2012

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How to get admin account on Galaxy
by kauerbach＠comcast.net 24 Aug '12

24 Aug '12

Hello, Can you tell me how to become an 'admin' user on Galaxy, or else change the current admin? Thank you. -Ken.

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Re: [galaxy-dev] How to speed up job execution
by Hans-Rudolf Hotz 24 Aug '12

24 Aug '12

On 08/24/2012 06:59 PM, kauerbach(a)comcast.net wrote: > That's very helpful. Thank you. I'm new to Galaxy. Can you tell me how > to become an 'admin' user and/or change the current admin user? > again, change the settings in "universe_wsgi.ini" by adding your e-mail (the one you use to log into Galaxy): #admin_users = foo(a)bar.com Regards, Hans > Thank you. > > -Ken. > > ------------------------------------------------------------------------ > > *From: *"Hans-Rudolf Hotz" <hrh(a)fmi.ch> > *To: *kauerbach(a)comcast.net > *Cc: *galaxy-dev(a)lists.bx.psu.edu > *Sent: *Friday, August 24, 2012 12:39:07 PM > *Subject: *Re: [galaxy-dev] How to speed up job execution > > > > On 08/24/2012 05:22 PM, kauerbach(a)comcast.net wrote: > > Hello, > > > > On our local instance of Galaxy jobs are taking an extremely long time > > to run, or they are not run at all. In the history it always says "job > > is waiting to run", even simple jobs like reformatting text files to be > > tab delimited. Is there a way to 1) check the Galaxy job queue, and 2) > > perhaps modify some parameters to speed up processing? > > > > Any suggestions would be greatly appreciated. > > > > Hi Kenneth > > Usually, Galaxy is not slow, but the tools executed by Galaxy are slow > (eg due to bad IO performance of the host server). > > "job is waiting to run" indicates there are unfinished jobs in the > queue. There are two ways to check the queue: > > If you are an 'Admin', select the Admin tab -> "Manage jobs". This will > list all running jobs. And you can kill jobs as well. > > Or use the galaxy report tools and have a look at "Today's jobs" > > > > Depending on your set-up, you might consider changing "universe_wsgi.ini": > > # Number of concurrent jobs to run (local job runner) > local_job_queue_workers = 5 > > to allow more parallel jobs > > > > Hope this helps > Hans > > > > > Thank you. > > > > > > > > > > ___________________________________________________________ > > 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: > > > > http://lists.bx.psu.edu/ > > >

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How to speed up job execution
by kauerbach＠comcast.net 24 Aug '12

24 Aug '12

Hello, On our local instance of Galaxy jobs are taking an extremely long time to run, or they are not run at all. In the history it always says "job is waiting to run", even simple jobs like reformatting text files to be tab delimited. Is there a way to 1) check the Galaxy job queue, and 2) perhaps modify some parameters to speed up processing? Any suggestions would be greatly appreciated. Thank you.

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Issue configuring reports_wsgi.ini
by Iry Witham 24 Aug '12

24 Aug '12

Hi Team, I am attempting to get the reports interface for my galaxy server to function. I have my reports.wsgi.ini configured so: # ---- HTTP Server ---------------------------------------------------------- [server:main] use = egg:Paste#http port = 9001 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # ---- Galaxy Webapps Report Interface ------------------------------------------------- [app:main] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.webapps.reports.buildapp:app_factory log_level = DEBUG # Database connection # Galaxy reports are intended for production Galaxy instances, so sqlite is not supported. # You may use a SQLAlchemy connection string to specify an external database. database_connection = postgres:///galaxy_1 # Where dataset files are saved file_path = database/files # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = database/tmp # Session support (beaker) use_beaker_session = True session_type = memory session_data_dir = %(here)s/database/beaker_sessions session_key = galaxysessions session_secret = changethisinproduction # Configuration for debugging middleware # debug = true use_lint = false # NEVER enable this on a public site (even test or QA) # use_interactive = true # path to sendmail # sendmail_path = /usr/sbin/sendmail # Address to join mailing list # mailing_join_addr = galaxy-user-join(a)bx.psu.edu<mailto:galaxy-user-join@bx.psu.edu> # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True # Profiling middleware (cProfile based) ## use_profile = True # Mail smtp_server = smtp.jax.org error_email_to = cbr-help(a)jax.org<mailto:cbr-help@jax.org> # Use the new iframe / javascript based layout use_new_layout = true # Serving static files (needed if running standalone) static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue The reports_webapp.log shows no errors but the process never completes loading. I stop the process manually after 20 minutes or more and no reports interface: python path is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-20 13:03:04,572 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,297 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,310 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,354 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,379 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,418 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,430 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,433 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,443 Enabling 'recursive' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,590 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,601 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,601 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,614 Enabling 'x-forwarded-host' middleware Starting server in PID 15823. serving on http://127.0.0.1:9001 Removing PID file reports_webapp.pid I am not sure what is going on, but I need to get this working again. Any help would be greatly appreciated. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Galaxy as an API IDE. (Incredibly insecure but possible)
by Ross 24 Aug '12

24 Aug '12

Anyone developing API scripts who likes to live dangerously - please read on. I just tested and blend-lib api scripts work fine in Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Compared with running in a console, you get persistence and other framework benefits plus at no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please! Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below. Took me a few iterations to develop the example - after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script I ran was persisted - ready to be edited and rerun easily - handy being able to quickly inspect dicts to help move progressively deeper iteratively. Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. =============Eg tool factory api script======================= import sys from blend.galaxy import GalaxyInstance ourGal = 'http://x.x.x.x:xxxx' ourKey = 'xxx' gi = GalaxyInstance(ourGal, key=ourKey) libs = gi.libraries.get_libraries() res = [] for lib in libs: #u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name': u'Demonstration sample RNA data', res.append('%s:\n' % lib['name']) res.append(str(gi.libraries.show_library(lib['id'],contents=True))) outf=open(sys.argv[2],'w') outf.write('\n'.join(res)) outf.close() returns a history item with: Demonstration sample RNA data:[{u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/F8de0c7750d06c0d0', u'type': u'folder', u'name': u'/', u'id': u'F8de0c7750d06c0d0'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/F7d480bbb847db8d0', u'type': u'folder', u'name': u'/rnaseq demo data', u'id': u'F7d480bbb847db8d0'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/8b25a086f3d48921', u'type': u'file', u'name': u'/rnaseq demo data/hg19_exons_mergedGENENAMES.bed', u'id': u'8b25a086f3d48921'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/5091b660e3557a3e', u'type': u'file', u'name': u'/rnaseq demo data/Select first on Ctrl_HAEC_FC078_1_sequence.txt (data 1)', u'id': u'5091b660e3557a3e'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/4e084a2837e50c40', u'type': u'file', u'name': u'/rnaseq demo data/Select first on Ctrl_HAEC_FC078_4_sequence.txt (data 4)', u'id': u'4e084a2837e50c40'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/0ab9ae3dbe24ad04', u'type': u'file', u'name': u'/rnaseq demo data/Select first on Ctrl_HAEC_FC079_1_sequence.txt (data 7)', u'id': u'0ab9ae3dbe24ad04'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/0a773730795f59a9', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HG_HAEC_FC078_2_sequence.txt (data 2)', u'id': u'0a773730795f59a9'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/c810c4dc5aed60ac', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HG_HAEC_FC078_5_sequence.txt (data 5)', u'id': u'c810c4dc5aed60ac'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/ee5b8d53fd29c05c', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HG_HAEC_FC079_2_sequence.txt (data 8)', u'id': u'ee5b8d53fd29c05c'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/1e04e5f52ca2af6e', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HN_HAEC_FC078_3_sequence.txt (data 3)', u'id': u'1e04e5f52ca2af6e'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/7e05ba393ab04bc6', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HN_HAEC_FC078_6_sequence.txt (data 6)', u'id': u'7e05ba393ab04bc6'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/335753abc7341224', u'type': u'file', u'name': u'/rnaseq demo data/Select first on HN_HAEC_FC079_3_sequence.txt (data 9)', u'id': u'335753abc7341224'}, {u'url': u'/galaxy/api/libraries/441d8112651dc2f3/contents/09c975479974360d', u'type': u'file', u'name': u'/smalltest.sam', u'id': u'09c975479974360d'}]Public data:[{u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F37c082b4cb3811bd', u'type': u'folder', u'name': u'/', u'id': u'F37c082b4cb3811bd'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F5390d290c0aca35b', u'type': u'folder', u'name': u'/1000 genomes and other public fastq and bam samples', u'id': u'F5390d290c0aca35b'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/721cc53ac555050e', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/ ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq', u'id': u'721cc53ac555050e'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/a96ce863d2b9a69a', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/ ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq(data 10)_FastQC.html', u'id': u'a96ce863d2b9a69a'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/81d4a112e7668435', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/1000g paired sample chr20', u'id': u'81d4a112e7668435'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/00776454b8f394c8', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/1000g chrom 10 single QC sample', u'id': u'00776454b8f394c8'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0ff2a12d5b5e045a', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/1000g sample chr1 single ended reads', u'id': u'0ff2a12d5b5e045a'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/8b394966390e7e29', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/Galaxy_GM12878.fastqillumina', u'id': u'8b394966390e7e29'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1b82079d07b4928f', u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam samples/Galaxy_GM12878.fastqilluminaFastQC.html', u'id': u'1b82079d07b4928f'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F2ef8c0af274c514d', u'type': u'folder', u'name': u'/BioMart', u'id': u'F2ef8c0af274c514d'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1ba8da1da6710cd5', u'type': u'folder', u'name': u'/BioMart/RefSeq2GeneName', u'id': u'F1ba8da1da6710cd5'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b5e989c148cd0aa1', u'type': u'file', u'name': u'/BioMart/RefSeq2GeneName/mm9_Names_RefSeq.txt', u'id': u'b5e989c148cd0aa1'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F6cd82b8eed63ee9a', u'type': u'folder', u'name': u'/encode', u'id': u'F6cd82b8eed63ee9a'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F177c1b293cbb701a', u'type': u'folder', u'name': u'/encode/FAIRE', u'id': u'F177c1b293cbb701a'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/ee24d81f0dee6a46', u'type': u'file', u'name': u'/encode/FAIRE/FASTQ Groomer on data 1', u'id': u'ee24d81f0dee6a46'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/f4209c75ea186d52', u'type': u'file', u'name': u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id': u'f4209c75ea186d52'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/cca5cab06be4a64c', u'type': u'file', u'name': u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id': u'cca5cab06be4a64c'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fa72f7b1e35fa5a2e', u'type': u'folder', u'name': u'/EpiDfiles', u'id': u'Fa72f7b1e35fa5a2e'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/fa29d7e45271edc8', u'type': u'file', u'name': u'/EpiDfiles/c2.all.v2.5.symbols.gmt', u'id': u'fa29d7e45271edc8'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/42a6cd9d5e1f6e99', u'type': u'file', u'name': u'/EpiDfiles/hg18_refSeq_HUGO_TSS.bed', u'id': u'42a6cd9d5e1f6e99'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/5d3a4056a308beac', u'type': u'file', u'name': u'/EpiDfiles/msigdb.v2.5.symbols.gmt', u'id': u'5d3a4056a308beac'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/02f72b1bb3982091', u'type': u'file', u'name': u'/EpiDfiles/msigdb.v3.0.symbols.gmt', u'id': u'02f72b1bb3982091'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1bae78f62566eb60', u'type': u'folder', u'name': u'/hg18', u'id': u'F1bae78f62566eb60'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/d6f2ea9a5a8e9773', u'type': u'file', u'name': u'/hg18/hg18_all_mrna_refseq_bed', u'id': u'd6f2ea9a5a8e9773'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F9f9703d25abcbc83', u'type': u'folder', u'name': u'/hg19', u'id': u'F9f9703d25abcbc83'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/100c928820ad6752', u'type': u'file', u'name': u'/hg19/Aceview acembly all hg19 exons', u'id': u'100c928820ad6752'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/aa8ad982a2157051', u'type': u'file', u'name': u'/hg19/Ensemble_Exon.bed', u'id': u'aa8ad982a2157051'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/9d7f80d7fdcd55af', u'type': u'file', u'name': u'/hg19/hg19_exons_mergedAnno.bed', u'id': u'9d7f80d7fdcd55af'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/45d26ffe370a9ca5', u'type': u'file', u'name': u'/hg19/hg19_exons_merged.bed', u'id': u'45d26ffe370a9ca5'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/dc7b5adeccaa6f0c', u'type': u'file', u'name': u'/hg19/hg19_exons_mergedGENENAMES.bed', u'id': u'dc7b5adeccaa6f0c'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/9ff231da824ea0fd', u'type': u'file', u'name': u'/hg19/hg19_transcriptome.bed', u'id': u'9ff231da824ea0fd'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1cdbace110dad0e6', u'type': u'file', u'name': u'/hg19/mirbase_wgRNA_tRNA_rnaGene.fa', u'id': u'1cdbace110dad0e6'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/cc4f723ba6129868', u'type': u'file', u'name': u'/hg19/RefSeq_Exon.bed', u'id': u'cc4f723ba6129868'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/2b827a488c9d67ec', u'type': u'file', u'name': u'/hg19/refseq hg19 exons ', u'id': u'2b827a488c9d67ec'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b99c33bfcc32f3f1', u'type': u'file', u'name': u'/hg19/small_RNA_UCSC_hg19.bed', u'id': u'b99c33bfcc32f3f1'}, {u'url': u'/galaxy/api/libraries/37c082b4cb3811bd/contents/60d6a0a8c6109c87', u'type': u'file', 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1 0

patch for vcf QUAL field with missing value "." in lib/galaxy/visualization/tracks/data_providers.py
by Jim Johnson 23 Aug '12

23 Aug '12

The VCF format ( http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-varian… ) specifies "." to represent missing values. lib/galaxy/visualization/tracks/data_providers.py throws an float conversion error when the qual field of a vcf file has the missing value: "." This can be remedied with the following patch, trackster handles the "None" value when displaying the variant. diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 2012 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 2012 -0500 @@ -634,7 +634,7 @@ # TODO? VCF does not have strand, so default to positive. "+", new_seq, - float( feature[5] ) ] + None if feature[5] == '.' else float( feature[5] ) ] rval.append(payload) return { 'data': rval, 'message': message }

2 1

Running a Java JDBC program from galaxy
by Robinson, Peter 23 Aug '12

23 Aug '12

Hi, I would like to run a Java program that accepts a VCF file from Galaxy and uses a JDBC connection to a postgreSQL database to do some analysis. The program should procude an HTML table that is then displayed in the Galaxy browser window. We have a local Galaxy server, and I have added my program to it using a configuration file. When I start the program via the framework, it just hangs, and "runs" forever (the command line version finishes in a few seconds). I am relatively new to Galaxy and have not been able to find out how to trouble shoot this in the documentation. Some questions: 1) The tables in the postgreSQL database have been set to GRANT SELECT TO PUBLIC, and the Java program is connecting to the database with the name and password of the owner of the database. Are there any other permissions issues that result from the Galaxy framework? 2) Is there some way of following program execution from a shell to see what Galaxy is doing? 3) Any other ideas? thanks Peter PD Dr. med. Peter N. Robinson, MSc. Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson(a)charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651

1 0

egg distribution error when running galaxy-central
by Clare Sloggett 23 Aug '12

23 Aug '12

Hi all, I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code. I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3. I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were: - create a virtualenv environment and activate it - get galaxy-dist and call run.sh - it asked me to build quite a lot of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems. - shut down galaxy-dist, and in another directory, get galaxy-central and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following: (galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed. Any idea what is causing this? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

4 8

metaphlan + krona = working
by Langhorst, Brad 23 Aug '12

23 Aug '12

Well.. it turned out to be pretty easy thanks to the efforts of Dannon and Brian Ondov I've added the metaphlan2krona.py script to the metaphlan toolshed repo. diff -r e88fa24fa837 metaphlan.xml --- a/metaphlan.xml Wed Jun 06 10:41:23 2012 -0400 +++ b/metaphlan.xml Wed Aug 22 21:36:21 2012 -0400 @@ -14,7 +14,7 @@ </command> <inputs> - <param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> + <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> <param name="PresetsForBowtie2" type="select" format="text"> <label>Sensitivity options for read-marker similarity (as described by BowTie2)</label> <option value="very-sensitive-local">Very Sensitive Local</option> diff -r e88fa24fa837 metaphlan2krona.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan2krona.py Wed Aug 22 21:36:21 2012 -0400 @@ -0,0 +1,49 @@ +#!/usr/bin/env python + +# ============================================================================== +# Conversion script: from MetaPhlAn output to Krona text input file +# Author: Daniel Brami (daniel.brami(a)gmail.com<mailto:daniel.brami@gmail.com>) +# ============================================================================== + +import sys +import optparse +import re + +def main(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' ) + parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krons output file name' ) + ( options, spillover ) = parser.parse_args() + + if not options.profile or not options.krona: + parser.print_help() + sys.exit() + + re_candidates = re.compile(r"s__|unclassified\t") + re_replace = re.compile(r"\w__") + re_bar = re.compile(r"\|") + + metaPhLan = list() + with open(options.profile,'r') as f: + metaPhLan = f.readlines() + f.close() + + krona_tmp = options.krona + metaPhLan_FH = open(krona_tmp, 'w') + + for aline in (metaPhLan): + if(re.search(re_candidates, aline)): + x=re.sub(re_replace, '\t', aline) + x=re.sub(re_bar, '', x) + + x_cells = x.split('\t') + lineage = '\t'.join(x_cells[0:(len(x_cells) -1)]) + abundance = float(x_cells[-1].rstrip('\n')) + + metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage)) + + metaPhLan_FH.close() + +if __name__ == '__main__': + main() diff -r e88fa24fa837 metaphlan_to_krona.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan_to_krona.xml Wed Aug 22 21:36:21 2012 -0400 @@ -0,0 +1,17 @@ +<tool id="meta_to_krona" name="MetaPhlAn to Krona" version="1.0.0"> + <description>Converter</description> + <command interpreter="python"> +metaphlan2krona.py -p $input -k $output + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + </tests> + <help> + MetaPhlAn to Krona Converter + </help> +</tool> To get it to work with krona i extended the krona repo like this diff -r 42c899125802 krona/krona.xml --- a/krona/krona.xml Mon Mar 19 17:39:59 2012 -0400 +++ b/krona/krona.xml Wed Aug 22 21:39:17 2012 -0400 @@ -7,15 +7,18 @@ ktImportBLAST -e ${type.factor} ${type.random} + #else if $type.program == 'krona': + ktImportText #else ktImportTaxonomy ${type.summary} #end if - -o $output + -o $output ${type.include} + #unless $type.program == 'krona' + -d $depth + #end unless - -d $depth - ## uncomment for isolated intranets (see README) ## ##-u /static/krona @@ -36,6 +39,7 @@ <option value="galaxy">Galaxy taxonomic representation</option> <option value="blast">Tabular BLAST results</option> <option value="taxonomy">Taxonomy ID list</option> + <option value="krona">Krona format</option> </param> <when value="galaxy"> <param name="factor" type="hidden" value=""/> @@ -51,6 +55,10 @@ <param name="summary" type="boolean" truevalue="-m 1" falsevalue="" label="Summarized" help="The first column is counts rather than query IDs."/> <param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/> </when> + <when value="krona"> + <param name="factor" type="hidden" value=""/> + <param name="include" type="hidden" value=""/> + </when> </conditional> <param name="depth" label="Depth" type="integer" help="The maximum depth to show in the chart (0 for unlimited)." value="0"/> <conditional name="datasets"> now i see this kind of graph [cid:D121407D-64B6-4D03-AE23-9DC53B52B5DC@home.langhorst.com] one more item.. had to add sanitize_all_html = False to universe_wsgi.ini brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

1 0

metaphlan + krona = ?
by Langhorst, Brad 22 Aug '12

22 Aug '12

I have installed both krona and metphlan from the toolshed to my local insttance. both seem to work ok, but I don't seen an easy way to get the metaphlan output into a form that krona can accept. has anybody solved this problem already? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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galaxy-dev August 2012