May 2014 - galaxy-dev - lists.galaxyproject.org

replacing XML fragments in mycustomtool.xml
by Pierre Lindenbaum 19 May '14

19 May '14

This question was cross-posted on https://biostar.usegalaxy.org/p/7619/ "Adding custom tools: resolving (external ) XML entities" I'd like to replace fragments of XML code in my custom tool declaration. My first idea was to use XML entities but it seems that the XML engine doesn't resolve them. (BTW: I know I can replace/declare things in $PATH and tool_dependencies.xml ) Another idea was to use <macros><token...> but I cannot make it work (see https://gist.github.com/lindenb/b2a04e0fefd4d295dba9 ) my macros definition: <?xml version="1.0"?> <macros> <token name="@JAVA_EXE@">/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java</token> <token name="@JVM_OPTIONS@">-Xmx500m</token> </macros> my tool definition: as a test, I echoed the value of @JAVA_EXE@ in /tmp/galaxy.txt (the macro was *not replaced* ) <?xml version="1.0" encoding="UTF-8"?> <tool id="com_github_lindenb_jvarkit_tools_misc_VcfHead" name="VcfHead" version="e098748b85acd5158a1ce612bd3d46e60948b9db" hidden="false"> <description>Print the first lines of a VCF</description> <macros> <import>jvarkit_macros.xml</import> </macros> <command>echo "@JAVA_EXE@" > /tmp/galaxy.txt && zcat -f ${input} | @JAVA_EXE@ @JVM_OPTIONS@ -cp /commun/data/packages/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/commun/data/packages/htsjdk/dist/htsjdk-1.112.jar:/commun/data/packages/htsjdk/dist/commons-jexl-2.1.1.jar:/commun/data/packages/htsjdk/dist/commons-logging-1.1.1.jar:/commun/data/packages/jvarkit-git/vcfhead.jar com.github.lindenb.jvarkit.tools.misc.VcfHead -n ${number} 2> /dev/null > ${output}</command> <inputs> <param format="vcf" name="input" type="data" label="Source VCF" optional="false"/> <param name="number" type="integer" value="10" label="Number of rows" optional="true"/> </inputs> <outputs> <data format="input" name="output" metadata_source="input"/> </outputs> <help>see https://github.com/lindenb/jvarkit/wiki/VcfHead</help> </tool> the output of 'hg tip' changeset: 9312:788cd3d06541 tag: tip parent: 9310:19f6e62bd372 parent: 9311:d7f37a2fe690 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 08 12:30:08 2013 -0400 summary: Merged stable. what's wrong in my <macros> definition ? Thanks. Pierre

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monitoring jobs start time
by Neil.Burdett＠csiro.au 19 May '14

19 May '14

Hi, I am currently using the reports tool to see what jobs have been executed etc ... When you look at the information for each job it states the time the job was put on the queue (creation time) not the actual start time of the job. Do you know if the start time of the job is stored somewhere? Thanks Neil

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nginx configuration question
by ruiwang.sz 17 May '14

17 May '14

Hi All, I have been trying to get the visualization through ucsc main working, thus I installed the nginx on our ubuntu(the one comes with update), then I configured it according to the wiki https://wiki.galaxyproject.org/Admin/Config/nginxProxy Here is the section in my nginx.conf include /etc/nginx/conf.d/*.conf; #include /etc/nginx/sites-enabled/*; upstream galaxy_app { server localhost:20020; } server { client_max_body_size 10G; # ... other server stuff ... location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } } server { location /_x_accel_redirect/ { internal; alias /; } } A couple notes: 1. I commented out #include /etc/nginx/sites-enabled/*; should I? 2. I have two sections of 'server', I am not sure if this is correct, but the wiki does not talk about it. I also have the following in universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect Now, if I go to http://127.0.0.1, it will redirect to http://127.0.0.1:20020, our galaxy instance, which is right. However, when i choose 'display in UCSC main' on a bigwig file, it failed to show and here is the log: 75.142.102.9 - - [16/May/2014:09:18:20 -0700] "GET /display_application/360b40e91c77a7e9/ucsc_bigwig/main HTTP/1.0" 302 - " http://128.125.28.215/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.137 Safari/537.36" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "GET /display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/param/track HTTP/1.0" 200 201 "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig HTTP/1.0" 200 92543742 "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /_x_accel_redirect/home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c" 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /galaxy/display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c" I don't know how this works -- the dataset I clicked is in fact: /home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat and it is on disk. However, it gave 404: 128.114.119.135 - - [16/May/2014:09:18:20 -0700] "HEAD /_x_accel_redirect/home/bioinfoadmin/app/galaxy-dist/database/files/003/dataset_3353.dat HTTP/1.0" 404 - "-" "genome.ucsc.edu/net.c" seems '_x_accel_redirect' is not substituted by the redirect alias '/'? but why? I checked the permission and it is 775 for all the dir on path, and 664 for dataset_3353.dat so www-data user has the read access. Also, where is this dir and file? /display_application/360b40e91c77a7e9/ucsc_bigwig/main/6e1547da5bd290c9/data/galaxy_360b40e91c77a7e9.bigwig I don't see them anywhere on the disk at all! I'm very confused about this. Could anyone give me a hand? I'll really appreciate! Thanks, Rui

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New tool listed under "Latest revision: failing tool tests" yet not tested
by Peter Cock 16 May '14

16 May '14

Hi Dave et al, Yesterday I uploaded a new tool to the TestToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Development repository: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh It is currently listed under "Latest revision: failing tool tests", Name Latest Installable Revision Owner blast_rbh 1 (2014-05-15) peterjc On viewing the tool, there are no test results at all (yet). Is this a corner case false-positive, or was there really a failed test run which is not being shown? Thanks, Peter

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$GALAXY_SLOTS is set incorrectly when using LSF
by Sytchev, Ilya 15 May '14

15 May '14

Hi, I've noticed that $GALAXY_SLOTS that was always set to 1 when using LSF. It turns out that LSF specifies the number of parallel slots using $LSB_DJOB_NUMPROC env variable which isn't checked in lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh. A diff that describes the fix is attached. Ilya

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User information when creating a new user
by Neil.Burdett＠csiro.au 15 May '14

15 May '14

Hi, when a new user creates a new account they only need an email address and password. This can be quite tricky to identify the user/demographics etc at a alter point. Is there a form that a user may complete where he could add optional data such as name, institution, address etc ? There is a table (user_address) that stores this information just not sure how/if it's populated Thanks Neil

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Re: [galaxy-dev] Upload a file
by Peter Cock 15 May '14

15 May '14

Hi Robert, I'm not sure that is a good idea - the existing upload tool gets special treatment in many places in Galaxy (e.g. turning a history into a workflow), and is itself being partly replaced with the newer Galaxy work (there's a little icon above the tool panel to import data). Peter P.S. Don't forget to CC the galaxy-dev list. On Thu, May 15, 2014 at 4:59 PM, <def87(a)gmx.de> wrote: > Hi Peter, > > thanks for your reply. I think there is a little misunderstanding: I want to > implement the upload tool itself. > I have code from someone else who has used the upload_dataset tag (I cannot > just use his code because I want to modify something - but when I try to > re-implement everything myself I need documentation). And my problem is that > I do not find any documentation for this tag. > > Regards, > Robert > > Gesendet: Freitag, 09. Mai 2014 um 16:21 Uhr > Von: "Peter Cock" <p.j.a.cock(a)googlemail.com> > An: def87(a)gmx.de > Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> > Betreff: Re: [galaxy-dev] Upload a file > On Fri, May 9, 2014 at 12:46 PM, <def87(a)gmx.de> wrote: >> Hi, >> >> I am a student who's trying to implement a simple galaxy tool. I am trying >> to provide the user with the option of uploading a file. I have copied >> code >> from another tool ... > > The upload tool is special (and separate). Normally the user must > separately upload their file(s) or import them from a shared library > BEFORE trying to use any of the analysis tools. > > Peter

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Conditional parameters don't work with radio display
by Peter Cock 15 May '14

15 May '14

Hello all, I ran into a problem with a conditional select parameter not working when shown as a radio box - despite the HTML having refresh_on_change set: <div class="form-row"> <label for="dbtype">Molecule type of FASTA inputs:</label> <div class="form-row-input"><div><input type="radio" name="seq|dbtype" refresh_on_change="true" value="prot" id="seq|dbtype|prot" checked='checked'><label class="inline" for="seq|dbtype|prot">protein</label></div> <div><input type="radio" name="seq|dbtype" refresh_on_change="true" value="nucl" id="seq|dbtype|nucl"><label class="inline" for="seq|dbtype|nucl">nucleotide</label></div></div> <div style="clear: both;"></div> </div> The simple workaround of using a drop-box select box instead worked, e.g. https://github.com/peterjc/galaxy_blast/commit/f70245e25ce171e1508585baea19… Is this something anyone else has noticed? Should I file an issue? Thanks, Peter -- This is what I was testing with initially, $ hg branch default $ hg log -b default | head changeset: 13855:215f23b27be9 tag: tip user: Carl Eberhard <carlfeberhard(a)gmail.com> date: Tue Mar 18 16:14:52 2014 -0400 summary: Page-embedded histories: allow embedding the same history more than once by removing the reliance on DOM ids and selecting/traversing based on sibling relation of the history's script I updated, same problem: $ hg log -b default | head changeset: 14501:75be6c49a65d tag: tip user: guerler date: Wed May 14 22:49:44 2014 -0400 summary: Charts: Fix style

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reports page download
by Neil.Burdett＠csiro.au 15 May '14

15 May '14

Hi, is there a way to download the information found on the reports page so it can be used in excel for example? Thanks Neil

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external chown does not chown multiple outputs .files_path
by Pavel Fibich 14 May '14

14 May '14

Dear developers, my Galaxy instance runs jobs under real users (DRMAA) and is going well with small problem. external_chown script does not change owner for files specified in inputs with .files_path suffix (i.e. directory for multiple output files; see https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files) After the end of job, whole job_working_directory/000/NO is properly re-owned to galaxy user, but files/000/dataset_NO.files remained owned by real user and are not accessible for galaxy user. Can you help me with this problem or give me any advise? I guess it will be something in lib/galaxy/jobs/__init__.py where re-owning is triggered. My galaxy instance was updated Apr 17 2014. All the best, Pavel -- ===*** Pavel Fibich pavel.fibich(a)prf.jcu.cz ++420-38-777-2374 Botany, Faculty of Science, University of South Bohemia Na Zlate stoce 1, 370 05 Ceske Budejovice, Czech republic ***===

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