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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">

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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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tool input is folder rather than file
by Pankaj Narang 24 Jul '13

24 Jul '13

Dear Developers, I want to design a tool whose input is folder containing files and sub-folders. I was wandering which value should I assign to "TYPE" attribute of PARAM tag in INPUTS. -- Best regards, Pankaj Narang

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Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.
by Maddhi, Srinivas 24 Jul '13

24 Jul '13

[Copying the list]. -----Original Message----- From: <Maddhi>, Srinivas Maddhi <srinivas-maddhi(a)uiowa.edu> Date: Wednesday, July 24, 2013 10:01 AM To: "Perez, Ricardo" <ricky_pz2(a)neo.tamu.edu> Subject: Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file. >Hi Ricardo, > >Ensuring that the appropriate reference indices are present, properly >configured and selected when running bowtie2 might help address this >problem. > >-----Original Message----- >From: <Perez>, Ricardo <ricky_pz2(a)neo.tamu.edu> >Date: Wednesday, July 24, 2013 1:35 AM >To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: [galaxy-dev] Bowtie2 error: Creates a 62 kb file. > >>Dear all, >> >>Today we ran some problems when running bowtie2. When we run bowtie2, >>the run manages to complete. However, bowtie2 creates a 62kb file. >>The error log that we get is the following: >> >>galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job >>destination (destination id: local:///) >>galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched >>galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell >>command for dependency 'bowtie2' >>galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency >>on 'bowtie2', ignoring >>galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell >>command for dependency 'samtools' >>galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency >>on 'samtools', ignoring >>galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: >>bowtie2 --version &> >>/usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; >>python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py >> --num-threads="4" >>--output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da >>t >> >>--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C >>h >>r07.+ChrM.+rDNA_v12" --single-paired=paired >>--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da >>t >> >>--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da >>t >> -I 0 -X 250 --settings=preSet >>galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job >>destination (destination id: local:///) >>galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution >>finished: bowtie2 --version &> >>/usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; >>python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py >> --num-threads="4" >>--output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da >>t >> >>--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C >>h >>r07.+ChrM.+rDNA_v12" --single-paired=paired >>--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da >>t >> >>--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da >>t >> -I 0 -X 250 --settings=preSet >>galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external >>set_meta script for job 1483: >>/usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files >>/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . >>/usr/local/galaxy/galaxy-dist/universe_wsgi.ini >>/usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD >>/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/gal >>a >>xy.json >>/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/met >>a >>data_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-di >>s >>t/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAss >>o >>ciation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_di >>r >>ectory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/l >>o >>cal/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_r >>e >>sults_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dis >>t >>/database/job_working_directory/001/1483/metadata_over! >> ride_HistoryDatasetAssociation_1767_MZilrL >>165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] "GET >>/api/histories/ca8efa3c47500414 HTTP/1.1" 200 - >>"http://galaxy.tamu.edu/history" "Mozilla/5.0 (X11; Linux x86_64) >>AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 >>Chrome/25.0.1364.160 Safari/537.22" >>165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history HTTP/1.1" >>200 - "http://galaxy.tamu.edu/tool_runner/index" "Mozilla/5.0 (Macintosh; >>Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) >>Chrome/28.0.1500.71 Safari/537.36" >>165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET >>/api/histories/1ab12f1e464820dd HTTP/1.1" 200 - >>"http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X >>10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 >>Safari/537.36" >>165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET >>/history/get_display_application_links HTTP/1.1" 200 - >>"http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X >>10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 >>Safari/537.36" >>galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external >>set_meta for job 1483 finished >>galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata >>from file for: HistoryDatasetAssociation 1767 >> >>We currently have the most recent version of bowtie2 and samtools. >>Anyone know how to fix this? >> >>Thank you for your time, >>--Ricardo Perez >> >>___________________________________________________________ >>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/ >> >>To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >

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uninstalling migrated tool
by Shantanu Pavgi (Campus) 24 Jul '13

24 Jul '13

It seems like if we uninstall a migrated tool then it's entry in the migrated_tools_conf.xml file doesn't get deleted. Does it need to be removed manually? -- Thanks, Shantanu

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All processes are freezed
by Ali Sharifi Zarchi 24 Jul '13

24 Jul '13

Hi everybody Since yesterday all processes I have run on Galaxy main are waiting. The system displayed a message to contact a Galaxy admin, but I could find no other way rather than this mailing list. Is this freeze due to a public maintenance, or it's just my problem? Best wishes, Ali

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job_conf.xml workers
by Ido Tamir 24 Jul '13

24 Jul '13

Hi, what is the relationship between workers defined in universe and job_conf.xml? e.g.: [server:handler0] use = egg:Paste#http port = 9092 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 <plugins workers="4">  <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="10"/> </plugins> a) do I have to specify the sum of the workers in job_conf.xml in universe? e.g. 4 local, 10 drmaa => 14 threadpool_workers per handler? Or is universe overridden by job_conf.xml? b) How many concurrent jobs can I then expect to have concurrently? 14 per handler? thank you very much, ido

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BWA Illumina Mapping / BWA Reference Genome
by Moritz Juchler 24 Jul '13

24 Jul '13

Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a *hg19 reference genome* which I have locally under /genedata/human_genome_GRCh37/. trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/ > total 8486312 > -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa > -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb > -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann > -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt > -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac > -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa *bwa is installed and gives me:* > trr@portalmoritz:~> bwa > Program: bwa (alignment via Burrows-Wheeler transformation) > Version: 0.7.5a-r405 > Contact: Heng Li <lh3(a)sanger.ac.uk> Then I tried to follow this guide: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup to get the reference files and http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. This is my *$PATH* > trr@portalmoritz:~> echo $PATH > > /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 *In the universe_wsgi.ini I changed:* > tool_dependency_dir = /home/trr/galaxy-dist/tool_dependency_dir > debug = False > use_interactive = True > library_import_dir = /genedata/ > allow_library_path_paste = True > admin_users = ... This is my *tool_dependency_dir:* > trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa> ls -l > total 4 > drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 > lrwxrwxrwx 1 trr users 6 2013-07-16 14:17 default -> 0.7.4/ This is the* version folder of bwa:* > trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4> ls -l > total 8 > drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin > -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the *content of env.sh:* > trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4> cat env.sh > PATH="/home/trr/bwa-0.7.5a/:$PATH" > export PATH And this is the *content of the bin folder:* > trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4/bin> ls -l > total 3896 > -rw-r--r-- 1 trr users 6098 2013-07-16 14:18 bamlite.c > -rw-r--r-- 1 trr users 3124 2013-07-16 14:18 bamlite.h > -rw-r--r-- 1 trr users 24816 2013-07-16 14:18 bamlite.o > -rw-r--r-- 1 trr users 11508 2013-07-16 14:18 bntseq.c > -rw-r--r-- 1 trr users 2557 2013-07-16 14:18 bntseq.h > -rw-r--r-- 1 trr users 37440 2013-07-16 14:18 bntseq.o > -rwxr-xr-x 1 trr users 998217 2013-07-16 14:18 bwa > -rw-r--r-- 1 trr users 24225 2013-07-16 14:18 bwa.1 > -rw-r--r-- 1 trr users 9416 2013-07-16 14:18 bwa.c > -rw-r--r-- 1 trr users 1381 2013-07-16 14:18 bwa.h .... I got the xmls and .py from https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping and i didnt change them at all and put them into ~/galaxy-dist/*tools/sr_mapping * (since they were missing in this folder) > bwa_color_wrapper.xml > bwa_wrapper.py > bwa_wrapper.xml I added *bwa_index_color.loc and bwa_index.loc* to ~galaxy-dist/*tool-data* (they were missing as well, there* were no* bwa_index_color.loc.sample or bwa_index.lox.sample files!!!) I only have this single line in both bwa_index_color.loc and bwa_index.loc > trr@portalmoritz:~/galaxy-dist/tool-data> cat bwa_index_color.loc > #This is a sample file distributed with Galaxy that enables tools > # > #<unique_build_id> <dbkey> <display_name> <file_path> > hg19 hg19 hg19 /genedata/human_genome_GRCh37/hg19.fa (Spaces are actually tabs!) After all that, I neither have the "Map with BWA for Illumina<https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos…>" in my local Galaxy version, nor do I find the reference genome. If i missed on any required, please tell me, I will answer you as soon as possible. Sincerly Yours Moritz Juchler

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