Re: [galaxy-dev] validator type="empty_field" is not working within repeat tags
by Anmol Hemrom
Hi,
I was trying to enforce not to allow empty string as an input to text
field. It is working outside the repeat tags but not working within repeat
tags.
1) Working fine
<param name="input" type="text" label="Enter Name">
<validator type="empty_field"/>
</param>
2) Not Working within repeat tags.
<repeat name="test" title="Test">
<param name="input" type="text" label="Enter Name">
<validator type="empty_field"/>
</param>
</repeat>
Thanks
Anmol
On Fri, May 29, 2015 at 2:00 PM, Dave Clements <clements(a)galaxyproject.org>
wrote:
> Hi Anmol,
>
> The best place to post this question is the Galaxy Dev List <
> galaxy-dev(a)lists.galaxyproject.org>. You can also search to see if
> anyone has asked a similar question at
> https://galaxyproject.org/search/web/
>
> Thanks,
>
> Dave C
>
> On Fri, May 29, 2015 at 6:56 AM, <anmol.jh(a)gmail.com> wrote:
>
>> Hi,
>>
>> I was trying to enforce not to allow empty string as an input to text
>> field. It is working outside the repeat tags but not working within repeat
>> tags.
>> 1) Working fine
>>
>> <param name="input" type="text" label="Enter Name">
>> <validator type="empty_field"/>
>> </param>
>>
>> 2) Not Working within repeat tags.
>>
>> <repeat name="test" title="Test">
>> <param name="input" type="text" label="Enter Name">
>> <validator type="empty_field"/>
>> </param>
>> </repeat>
>>
>> Thanks
>>
>> Anmol
>>
>> _____________________________________
>> Sent from http://dev.list.galaxyproject.org
>>
>>
>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>
6 years, 2 months
Adding categories to Main
by Keith Suderman
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers,
Keith
------------------------------
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY
6 years, 2 months
Unable to run simple Docker tool
by Mikel Egaña Aranguren
Hi;
I'm trying to develop a Docker based tool, as suggested by a peer-reviewer
who might be reading this :P
However, I'm having trouble with even the most basic setting, and I don't
know what might be wrong, so any help will be much appreciated. I have
developed a very simple docker image and corresponding Galaxy tool, so that
I get it working before starting with the actual tool, but when I execute
it through Galaxy it simply stays executing forever, instead of failing or
terminating.
My image simply executes a shell script that reads the content of a file
and concatenates a string to it. The image:
FROM busybox:ubuntu-14.04
MAINTAINER Mikel Egaña Aranguren <mikel.egana.aranguren(a)gmail.com>
RUN mkdir /sadi
COPY test-io.sh /sadi/
RUN chmod a+x /sadi/test-io.sh
ENV PATH $PATH:/sadi
The test-io.sh script within the image:
#!/bin/sh
cat $1
echo "AAA"
Invoking the container and executing the script through a normal shell
works fine:
REPOSITORY TAG IMAGE
ID CREATED VIRTUAL SIZE
mikeleganaaranguren/busybox-galaxy-test-io v1
9c2b8bdade1d 54 minutes ago 5.609 MB
docker run -i -t mikeleganaaranguren/busybox-galaxy-test-io:v1
BusyBox v1.21.1 (Ubuntu 1:1.21.0-1ubuntu1) built-in shell (ash)
Enter 'help' for a list of built-in commands.
~ #
~ # echo "BBB" > test
~ # test-io.sh test
BBB
AAA
This is the tool file I'm using in Galaxy:
<tool id="SADIBUSYBOX" name="SADIBUSYBOX">
<description>IO</description>
<requirements>
<container
type="docker">mikeleganaaranguren/busybox-galaxy-test-io:v1</container>
</requirements>
<command>
test-io.sh $input > $output
</command>
<inputs>
<param name="input" type="data" label="Dataset"/>
</inputs>
<outputs>
<data format="txt" name="output" />
</outputs>
<help>
</help>
</tool>
And my job_conf.xml:
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="docker_local">
<destination id="local" runner="local"/>
<destination id="docker_local" runner="local">
<param id="docker_enabled">true</param>
</destination>
</destinations>
</job_conf>
As I said, when I execute the tool in Galaxy, it simply executes forever,
it stays in a "yellow state", till I kill the Galaxy server. The log says:
127.0.0.1 - - [18/Aug/2015:19:08:00 +0200] "GET
/tool_runner?tool_id=SADIBUSYBOX HTTP/1.1" 200 - "http://127.0.0.1:8080/"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101
Firefox/40.0"
galaxy.tools.actions INFO 2015-08-18 19:08:07,178 Handled output (77.825 ms)
galaxy.tools.actions INFO 2015-08-18 19:08:07,280 Verified access to
datasets (12.387 ms)
galaxy.tools.execute DEBUG 2015-08-18 19:08:07,307 Tool [SADIBUSYBOX]
created job [2] (217.508 ms)
127.0.0.1 - - [18/Aug/2015:19:08:07 +0200] "POST /api/tools HTTP/1.1" 200 -
"http://127.0.0.1:8080/tool_runner?tool_id=SADIBUSYBOX" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:07 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
galaxy.jobs DEBUG 2015-08-18 19:08:07,714 (2) Working directory for job is:
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2
galaxy.jobs.handler DEBUG 2015-08-18 19:08:07,721 (2) Dispatching to local
runner
galaxy.jobs DEBUG 2015-08-18 19:08:07,839 (2) Persisting job destination
(destination id: docker_local)
galaxy.jobs.runners DEBUG 2015-08-18 19:08:07,849 Job [2] queued (128.176
ms)
galaxy.jobs.handler INFO 2015-08-18 19:08:07,897 (2) Job dispatched
galaxy.jobs.command_factory INFO 2015-08-18 19:08:08,163 Built script
[/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh]
for tool
command[/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh]
galaxy.jobs.runners DEBUG 2015-08-18 19:08:08,322 (2) command is: sudo
docker inspect mikeleganaaranguren/busybox-galaxy-test-io:v1 > /dev/null
2>&1
[ $? -ne 0 ] && sudo docker pull
mikeleganaaranguren/busybox-galaxy-test-io:v1 > /dev/null 2>&1
sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy:ro
-v
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/tools/catDocker:ro
-v
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2:rw
-v
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files:rw
-w
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2
--net none --rm -u 1001 mikeleganaaranguren/busybox-galaxy-test-io:v1
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/tool_script.sh;
return_code=$?; python
"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/set_metadata_3aWBf9.py"
"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/tmp/tmpH2gy3X"
"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/galaxy.json"
"/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_WxbKNP,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_p8UK91,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_wPm09U,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_irSo7t,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/files/000/dataset_2.dat,/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_1glVfb"
5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2015-08-18 19:08:08,323 (2) executing job
script:
/home/mikel/UPV-EHU/SADI-Docker-Galaxy/galaxy/database/job_working_directory/000/2/galaxy_2.sh
galaxy.jobs DEBUG 2015-08-18 19:08:08,375 (2) Persisting job destination
(destination id: docker_local)
127.0.0.1 - - [18/Aug/2015:19:08:11 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:21 +0200] "GET
/history/current_history_json HTTP/1.1" 200 - "http://127.0.0.1:8080/"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0) Gecko/20100101
Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:21 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents?dataset_details=ebfb8f50c6abde6d%2C33b43b4e7093c91f%2Ca799d38679e985db%2C5969b1f7201f12ae%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2C03501d7626bd192f%2C3f5830403180d620%2Ce85a3be143d5905b%2Cc9468fdb6dc5c5f1%2C2a56795cad3c7db3
HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:40.0) Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:25 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:29 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:33 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:38 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:42 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
127.0.0.1 - - [18/Aug/2015:19:08:46 +0200] "GET
/api/histories/f2db41e1fa331b3e/contents HTTP/1.1" 200 - "
http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:40.0)
Gecko/20100101 Firefox/40.0"
Thanks!
--
Mikel Egaña Aranguren, Ph.D.
http://mikeleganaaranguren.com
6 years, 3 months
Get dataset/API ids for a dataset
by Asma Riyaz
Hello Galaxy-dev,
I thank you so much for all the help you have given me.
I have a question about data set ids in galaxy. As a background, I am
running my own galaxy instance on a server. A pipeline implemented in the
lab produces the following files in the history:
1) 2 BAM files
2) A JSON file
My goal is to use this JSON file to pass the path/URL of bam files into a
custom JS we wrote for visualization purpose.
This JSON file contains among many other details the paths/URLs to the
above bam files. I am using JSON filetypes to send data to the JS
visualization within Galaxy. To do this, I have my own JS which loads a BAM
file from URL provided into an IGV.js track. IGV.js, which is responsible
for making the tracks, expects a valid URL which is updated in the JSON
file in this manner:
1) Extract the API_key and history id from a loaded BAM file
2) Edit the JSON file to reflect the BAM file's dataset id to be something
like this:
{
"CLL-HL_pilot.r1.fastq": {
"DNA": "/datasets/36ddb788a0f14eb3/display?to_ext=bam",
...
This works fine if I know the API Key for bam files. When a pipeline
executes dataset ids are generated for each output. I want to access and
include these ids in the JSON file and load the updated JSON file into the
history with the bams. Is there a way to get the ids from the history in
this manner?
Thank you,
Asma
6 years, 3 months
login problems when using a proxy and serving at a subdirectory
by Bernau, Christoph
Dear all,
I have a problem with configuring my galaxy instance with a proxy server when I try to serve at a subdirectory.
I followed the description at https://wiki.galaxyproject.org/Admin/Config/nginxProxy
The basic configuration works just fine.
When I use the procedure described in the section
"serving galaxy at a subdirectory", the proxying principally also works.
However, when registered users try to log in to galaxy, galaxy will simply directs them to the starting page (which I think is
what normally happens after logging in) without displaying an error message. Nonetheless, users do not have access to the functionalities which only logged in users
can use. E.g. each time they try to use the "workflows"-button they are told to log in.
Could you please provide any help on this issue?
Cheers,
Christoph
6 years, 3 months
Rename output from a repeat
by Ulf Schaefer
Hi all
We frequently use the syntax below to rename outputs of workflows that
we run in batch. It is convenient to have sample names from fastqs
carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g.
the VelvetOptimiser. Does anybody know if there is a syntax to make this
work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot for your help
Ulf
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6 years, 3 months
samtools dependency changes ?
by Wolfgang Maier
Dear all,
with older Galaxies (prior to latest_15.03 I think), you could satisfy
Galaxy's samtools dependence for indexing bam files by having a samtools
executable in tool-dependencies/samtools/default/bin (with the
tool-dependencies directory declared as tool_dependency_dir in
galaxy.ini of course).
Now (checked with latest_15.03 and .05), this is not working any more!
The executable will still be used during bam uploads, but not when a bam
file gets created by a tool.
The reason is that before the job runner (tested this with the local job
runner only) used to build the dependency shell command for dependency
'samtools' before finishing a job, but now the job wrapper finish method
fails because it naively expects to find samtools on $PATH.
Best,
Wolfgang
6 years, 3 months
Galaxy and PBS/Torque Cluster
by Ryan Johnson
Hello All,
We are using a Bio-Linux 8 Galaxy instance and are currently trying to
integrate in into a PBS/Torque cluster. Currently we are able to run
jobs locally but not via PBS. Can anyone provide us with a step by step
guide to configure Galaxy and the PBS.
I have included some of the errors we are receiving below:
galaxy.datatypes.metadata DEBUG 2015-08-19 14:56:42,920 Failed to
cleanup MetadataTempFile temp files from
/usr/lib/galaxy-server/database/job_working_directory/000/96
/metadata_out_HistoryDatasetAssociation_100_Kk1ajw: No JSON object could
be decoded
galaxy.jobs.runners.pbs ERROR 2015-08-19 14:56:42,960 Connection to PBS
server for submit failed: 0: no error
We can not figure out what is stopping our jobs from entering the PBS
queue. Below is our job_conf.xml.
<?xml version="1.0"?>
<job_conf>
<plugins workers="2">
<!-- 'workers' is the number of threads for the runner's work queue. -->
<!-- The default from <plugins> is used if not defined for a <plugin> -->
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
</plugins>
<handlers>
<handler id="main"/>
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini -->
</handlers>
<destinations default="defaultq">
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources -->
<destination id="defaultq" runner="pbs" tags="cluster">
<param id="-q">defaultq</param>
<param id="-l">walltime=24:00:00</param>
</destination>
</destinations>
</job_conf>
Thank you very much for all the assistance!
Regards,
Ryan
--
Ryan S. Johnson, PhD
Applications Scientist
Center for Advanced Research Computing
P: (650) 430-6194
E:rjohns03@carc.unm.edu
6 years, 3 months
Change genome build for multiple files
by Frederik Coppens
Hi
is there a convenient way to change the genome build for a lot of files at once (e.g. a whole data library)?
I want to ‘update’ to a newer genome build and the only way I found is to go through ‘Edit information’ for each file separately. I assume it can be changed directly in the db, but I’m not familiar with the scheme.
thanks
Frederik
==================================================================
Frederik Coppens, Ph.D.
Project Leader Applied Bioinformatics & Biostatistics
IT manager
Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809
VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent
Technologiepark 927, 9052 Gent, BELGIUM
frcop(a)psb.ugent.be http://www.psb.ugent.be/abb
==================================================================
6 years, 3 months
