galaxy-dev July 2013

galaxy-dev@lists.galaxyproject.org

133 participants
209 discussions

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 25 Jul '13

25 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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Re: [galaxy-dev] HTML output with external Javascrip
by Stewart, Andrew 25 Jul '13

25 Jul '13

>>The file that Gift is producing is already an html file and there's >>already an html datatype in Galaxy by default. The output file in >>question just invokes remote javascript libraries inside <script> tags, >>and this seems to be tripping up Galaxy's data viewer. > >Setting up relative paths to images and scripts inside your HTML output >should work; this is done in FastQC and other similar tools. > >>We've tried downloading and referencing the >>javascript libraries in /static/js as well. > >This should work as well and is the approach used by the rGenetics tools, >but the path you want is /static/scripts/ Note that Galaxy already >has >many jQuery libraries in /static/scripts/libs/jquery, which could >simplify development. > >>I know that the new visualization platform in Galaxy uses a lot of >>external javascript libraries like D3? does anyone know how that is being >>handled differently? > >For now, the viz framework is a different code base that's not relevant >for displaying datasets. > >Best, >J. Thanks Jeremy, we'll give this a shot. -Andrew -- Andrew Stewart Office of Research Information Services (ORIS), Office of the Chief Information Officer (OCIO), Smithsonian Institution 202-633-2840 On 7/25/13 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu" <galaxy-dev-request(a)lists.bx.psu.edu> wrote: >>The file that Gift is producing is already an html file and there's >>already an html datatype in Galaxy by default. The output file in >>question just invokes remote javascript libraries inside <script> tags, >>and this seems to be tripping up Galaxy's data viewer. > >Setting up relative paths to images and scripts inside your HTML output >should work; this is done in FastQC and other similar tools. > >>We've tried downloading and referencing the >>javascript libraries in /static/js as well. > >This should work as well and is the approach used by the rGenetics tools, >but the path you want is /static/scripts/ Note that Galaxy already has >many jQuery libraries in /static/scripts/libs/jquery, which could >simplify development. > >>I know that the new visualization platform in Galaxy uses a lot of >>external javascript libraries like D3? does anyone know how that is being >>handled differently? > >For now, the viz framework is a different code base that's not relevant >for displaying datasets. > >Best, >J. >

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plain text output format
by mark.rose＠syngenta.com 25 Jul '13

25 Jul '13

Hi All I'm trying to format one of the three outputs of my galaxy tool as plain text. Thus far no matter how I specify my output format in the tool xml file I have the same problem. When I click the eye icon it opens a save dialog rather that displaying the text output in the central frame. The preview shows the text output and if I follow through and save the output and open with wordpad it is fine. Also if I edit the attributes of the output and change it to "txt" (which is one of the formats I had tried specifying in the xml) it will render in the central frame but I would rather not have to do that. Both of my other outputs (a vcf and a tab-delimited file are rendered in the central frame properly). What can I do to fix this? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-dev] HTML output with external Javascript
by Stewart, Andrew 25 Jul '13

25 Jul '13

Hi Gromobir, The file that Gift is producing is already an html file and there's already an html datatype in Galaxy by default. The output file in question just invokes remote javascript libraries inside <script> tags, and this seems to be tripping up Galaxy's data viewer. We've tried turning off the the html sanitizer, as mentioned below, but this doesn't seem to have any effect. We've tried downloading and referencing the javascript libraries in /static/js as well. I know that the new visualization platform in Galaxy uses a lot of external javascript libraries like D3Š does anyone know how that is being handled differently? Thanks, Andrew -- Andrew Stewart Office of Research Information Services (ORIS), Office of the Chief Information Officer (OCIO), Smithsonian Institution 202-633-2840 On 7/23/13 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu" <galaxy-dev-request(a)lists.bx.psu.edu> wrote: >On 07/23/2013 05:14 PM, Sinthong, Phanwadee wrote: >>Hi galaxy-dev, >> >>I have a tool that generates a HTML output file which uses some >>javascript library. I cannot view the output file with the eye button in >>Galaxy, but it still works fine from the HTML file opened out of the >>file directory. >>I changed the sanitize_all_html = False and restarted the galaxy server >>as some earlier post suggested but still couldn't view the output file. >>What else can I do to execute Javascript in the Galaxy browser? >> >Which library are you trying to use? >You may have to define your own datatype and add something like the >following to the file "datatypes_conf.xml"afterwards: > ><datatype extension="html" type="galaxay.datatypes.xml:Html" >mimetype="application/html">

2 1

Lumi wrapper for Galaxy
by Sachit Adhikari 25 Jul '13

25 Jul '13

Hello group, I am trying to write lumi wrapper for Galaxy. Is anyone is writing or already have written lumi wrapper for Galaxy. I couldn't find in both galaxy main tool shed and test tool shed. Regards Sachit

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galaxy-dev July 2013