- galaxy-dev - lists.galaxyproject.org

Tool Shed Request - sanity check uploads?
by Peter Cock 29 Jul '13

29 Jul '13

Hi all, For what is I think the second time (fortunately this was only on the Test Tool Shed), I have managed to upload a tar-ball to the wrong repository: 2:fae4084a0bc0 http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired It could have been a glitch, but more likely is was simply inattention on my part (most likely - multiple tab browsing has its downsides). This leads me to offer some suggestions for how to prevent this kind of user error in future: (1) After the upload, show a preview of the changes for confirmation (the drawback is this could take a long time to process for a large upload, and lead to time outs). (2) After upload, before committing the changes, compare the tool contents - adding or removing some tools is normal, replacing ALL the tools with different tools is probably an error and should be subject to user confirmation. (3) Offer a repository action to revert to a prior commit (current workaround is to re-upload the old good file, which I did as 3:81ac324efa49 in this case). Peter

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GATK
by sridhar srinivasan 29 Jul '13

29 Jul '13

Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ also suggest me about the Rod file for dbSNP. Thanks Sridhar

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data snapshot is not the same on local instance of Galaxy
by Nikhil Mallela 29 Jul '13

29 Jul '13

Hi, A few days ago, I have installed the stable release of of Galaxy local instance on my Workstation & I am running it behind Apache web server proxy . In regard to the data snapshots, I've observed that, it is much more organized on the Galaxy main rather than on my local instance. For example, Take a look at these pictures: On my local instance: [image: Inline image 1] On the Galaxy main: (also, this [image: Inline image 4] is missing on my local instance) [image: Inline image 2] Also, when I click the view [image: Inline image 3] on my local instance,the headers of the data is not corresponding to its respective columns. So, how can I fine tune these ? Thanks in advance! Nikhil. -- Nikhil Vinod Mallela, PhD Student University of Muenster, Neil-Stensen Str. 12-14, 48149, Muenster, Germany.

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Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth
by Steve Harper 27 Jul '13

27 Jul '13

I'm trying to install Galaxy behind an Apache proxy using mod_auth_cas for user authentication. I've got a ways in but am now stuck with galaxy not getting the REMOTE_USER. Has anyone deployed with this module? I have use_remote_user = true on in my universe_wsgi.ini along with a valid maildomain. Here's my apache config: NameVirtualHost galaxy.utah.edu:80 NameVirtualHost galaxy.utah.edu:443 CASLoginURL https://go.utah.edu/cas/login CASValidateURL https://go.utah.edu/cas/serviceValidate CASValidateServer Off CASAllowWildcardCert On CASCertificatePath /etc/pki/tls/certs/ca-bundle.trust.crt CASCookiePath /var/run/mod_auth_cas/ CASTimeout 3600 CASIdleTimeout 1800 CASDebug On <VirtualHost 155.101.xx.40:80> RedirectPermanent / https://galaxy.utah.edu/ </VirtualHost> <VirtualHost galaxy.utah.edu:443> SSLEngine on SSLProtocol -ALL +SSLv3 +TLSv1 SSLCipherSuite HIGH:-aNULL:-eNULL # Export the SSL environment variables to scripts <Files ~ "\.(cgi|pl|shtml|phtml|php3?)$"> SSLOptions +StdEnvVars </Files> # Protocol adjustments for broken clients SetEnvIf User-Agent ".*MSIE.*" \ nokeepalive ssl-unclean-shutdown \ downgrade-1.0 force-response-1.0 SSLCertificateFile /etc/pki/tls/certs/wildcard.utah.edu.crt SSLCertificateKeyFile /etc/pki/tls/certs/wildcard.utah.edu.key SSLCertificateChainFile /etc/pki/tls/certs/gd_bundle.crt <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> AuthType CAS AuthName Galaxy Require valid-user # CASAuthNHeader REMOTE_SHMUSER # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) # RewriteCond %{LA-U:REMOTE_SHMUSER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e XSendFile on XSendFilePath / # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary RequestHeader set X-URL-SCHEME https </Location> <Location "/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> ServerName galaxy.utah.edu RewriteRule ^/static/style/(.*) /uufs/utah.edu/sys/pkg/galaxy/std/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /uufs/utah.edu/sys/pkg/galaxy/std/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /uufs/utah.edu/sys/pkg/galaxy/std/static/$1 [L] RewriteRule ^/favicon.ico /uufs/utah.edu/sys/pkg/galaxy/std/static/favicon.ico [L] RewriteRule ^/robots.txt /uufs/utah.edu/sys/pkg/galaxy/std/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] </VirtualHost> Any help is appreciated. Steve Harper Systems Administrator Center for High Performance Computing University of Utah

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Fwd: Intersect Tool
by Alexander Kurze 26 Jul '13

26 Jul '13

Dear All, I am running my own galaxy instance and I have been using the tool intersect (under the tab operate on genomic intervals) a few times successfully. However, recently I get following error message: /home/galaxy/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() I googled it and there was never a straight answer. Could anyon explain how to fix it or at least tell me what it means. Thank you for your help in advance. Keep up the great work! Best wishes, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341

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Regarding FTP configuration
by Patra, Jibesh 26 Jul '13

26 Jul '13

Hello all: I am setting up a local instance of galaxy server. I have followed the steps mentioned in the galaxy wiki regarding the setup. I have setup a proftpd server with postgresql authentication. But, I am getting 530 login incorrect error when trying to connect using a FTP client. I followed the solution of a similar problem given here: http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295… without any success. In the last post of the given link Mr. Tobias has posted some thing like this: "I followed the advice you offered back-channel and backed off the galaxy changes to support pbkdf2". I am unable to follow this part. For reference- My proftpd configuration: http://pastebin.com/LUjAyHvh proftpd SQL log: http://pastebin.com/2psTtnZv proftpd -l Compiled-in modules: mod_core.c mod_xfer.c mod_rlimit.c mod_auth_unix.c mod_auth.c mod_ls.c mod_log.c mod_site.c mod_delay.c mod_facts.c mod_auth_pam.c mod_sql.c mod_sql_postgres.c mod_sql_passwd.c mod_cap.c A solution will be appreciated. Thank you, -- Jibesh Patra

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BWA missing index on reference genome
by Moritz Juchler 26 Jul '13

26 Jul '13

Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: > -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict > -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta > -rw-r--r-- 1 trr users 6597 2013-07-25 19:41 human_g1k_v37.fasta.amb > -rw-r--r-- 1 trr users 6844 2013-07-25 19:41 human_g1k_v37.fasta.ann > -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt > -rw-r--r-- 1 trr users 2746 2013-07-25 11:32 human_g1k_v37.fasta.fai > -rw-r--r-- 1 trr users 775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac > -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa 5 and I changed the bwa_index and bw_index_color.loc to the path /genedata/human_genome_GRCh37/hg19.fa 6 This is my *$PATH* > trr@portalmoritz:~> echo $PATH > > /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 Is there anything I am missing? I would be glad about some help. Best Moritz

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Galaxy ego fetching error (Mac OS X 10.8)
by Iry Witham 26 Jul '13

26 Jul '13

Hi Team, I am attempting to rebuild my local instance of galaxy on my Mac since having been upgraded to Mountain Lion. I have installed Mercurial, postgres, python2.7. I have cloned the latest galaxy-dist. However, when I attempted to launch galaxy with sh run.sh it fails to complete the fetch. Here is what I get: milkyway:galaxy-dist itw$ sh run.sh Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing data_manager_conf.xml from data_manager_conf.xml.sample Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing universe_wsgi.ini from universe_wsgi.ini.sample Initializing tool-data/shared/ncbi/builds.txt from builds.txt.sample Initializing tool-data/shared/ensembl/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/publicbuilds.txt from publicbuilds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample Initializing tool-data/sam_fa_new_indices.loc from sam_fa_new_indices.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.4.2-py2.7.egg Fetched http://eggs.galaxyproject.org/Babel/Babel-0.9.4-py2.7.egg Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-p… Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.galaxyproject.org/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-0.2-py2.7.egg Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg Fetched http://eggs.galaxyproject.org/elementtree/elementtree-1.2.6_20050316-py2.7.… Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e99… Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg Fetched http://eggs.galaxyproject.org/boto/boto-2.5.2-py2.7.egg Fetched http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: mercurial==2.2.3 Fetch failed. I have also tried to run python ./scripts/fetch_eggs.py and get the following: milkyway:galaxy-dist itw$ python ./scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.galaxyproject.org/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 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/itw/work/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/itw/work/Galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/itw/work/Galaxy/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) I have looked through the Dev site and have found nothing that helps. Any ideas are welcome. Thanks, Iry Witham 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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Problems with tophat in local instance
by Rainy Luo 26 Jul '13

26 Jul '13

Hi,all, I am a beginner of Galaxy.Because I need to analyze large-scale NGS data and the pubic Galaxy serve did not work out,I installed linux(the first time to use linux) and set up the local galaxy instance in my computer. It seemed everything worked fine until I tried to use Tophat to align the reads to the reference genome.The problem is although I have already downloaded the Refgenome from UCSC,when I use the Tophat,"select a reference genome"option is empty(please see the attached file). is there anybody having similar problem?How to deal with it? Thanks! Rainy

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Trouble using enumerate within <command>
by Shafer, Christina 25 Jul '13

25 Jul '13

Hello, I'm trying to incorporate a pipeline tool into our instance of Galaxy. My tool xml uses the <repeat> tag to allow an end-user to enter a number of different fasta/fastq files with information about each of those files so that RSEM<http://deweylab.biostat.wisc.edu/rsem/> can be run on all of the files one at a time with minimal end-user input. My repeat name is Files. To do this, I need the tool xml to loop over each file and its input parameters to put together a string of input to a perl wrapper (file is in same directory as the xml). I tried using 'enumerate' to do this within the <command> tag with perl as the interpreter, but I'm noticing some some strange behavior with ordering of statements in the tag. Here's what I have for the tool xml's command tag (aforementioned perl wrapper is run-rsem-1.2.3.pl). <command interpreter="perl"> #for $i, $s in enumerate( $Files ) #if $s.input.fastqmatepair.matepair=="single" #/opt/galaxy/galaxy-dist-dev/tools/ngs_rna/run-rsem-1.2.3.pl --seed-length $s.seedlength --forward-prob $s.fprob -p $s.cpus --single_fastq $s.input.fastqmatepair.singlefastq /opt/galaxy/references/rhesus/rheMac2_ensembl_1.64/RSEM_rheMac2_ensembl_1.64 #if $s.need_bam.yes_bamfile=="yes": --output-genome-bam --bamfile $s.bam_res #end if #if $s.dostats.stat==1: --fragment-length-mean $s.dostats.fraglenmean --fragment-length-sd $s.dostats.fraglensd #end if #if $s.dorspd.rspd==1: --estimate-rspd --num-rspd-bins $s.dorspd.rspd_num #end if #end if #end for </command> I must be missing something above because it does not call run-rsem-1.2.3 for each loop iteration. Do I need a break or pause or something within the tag to make this enumerate loop work correctly? FWIW, to debug I added a print statement between the last '#end if' and the '#end for' above: 'print "loop iteration $i.\n";' and this correctly resulted in a number of separate calls to run-rsem-1.2.3, but the literal statement "print loop iteration #.\n" was also added as an argument to the perl wrapper that caused it to quit early because too many input arguments were received. Please let me know if anything needs clarification. Any help is much appreciated - thanks! Christina Shafer, Ph.D Bioinformatics Analyst Regenerative Biology Laboratory Morgridge Institute for Research

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