I would like to get source code with Mercurial of this tarballs :
galaxy-dist.b258de1e6cea.tar.gz, and not the latest source.
Is it possible to specify "b258de1e6cea" version with hg clone command ?
The aim is to update my copy of Galaxy wich have been locally installed
with a tarball in order to use, in the future, Mercurial and hg pull to
update Galaxy version.
Thanks a lot,
We are going to migrate to a new instance of the galaxy server. Our current
instance contains a number of workflows and other data that we would like
to have available on the new server. Is there a way to backup the workflows
and then reload them on the new server?
-Robert Paul Chase
I m running my own Galaxy instance and I would like to do some simple
customization of the web interface such as adding my logos in the header
frame, changing background colors, etc.
I am having a look to static/ folders but I can't see clearly where the
header frame is defined.
Could you please tell me if there is any tutorial for doing so? Any
starting point? Or which folder/file(s) corresponds to the web interface in
This is my code for running a samtools command internally, via Galaxy:
open INP,"< $ARGV"
or die "Cannot open file: $!";
$file = "$ARGV";
open OUT, "> $file"
or die "Cannot open file: $!";
@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV 2>&1`;
print OUT @out;
The 2>&1 is used to redirect the STDERR to STDOUT. When I run this in the
console, it gives a non-empty file. But when run it in Galaxy, Galaxy can
no longer find the path. This error message is given to me.
Traceback (most recent call last):
line 126, in run_job
job_wrapper.finish( stdout, stderr )
File "/home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line
618, in finish
dataset.set_meta( overwrite = False )
File "/home/applications/galaxy-dist/lib/galaxy/model/__init__.py", line
874, in set_meta
return self.datatype.set_meta( self, **kwd )
line 179, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
The weird thing is, when I remove the 2>&1 from the code and run it again
in Galaxy, I am able to get this diagnostic message:
[samopen] SAM header is present: 66338 sequences.
This is the reason why I added the 2>&1 in the first place, so that this
diagnostic message would be 'ignored' (since it is detected as an error).
Now, if the other code (the one without 2>&1) is able to produce the
aforementioned diagnostic message, then I assume that it is able to at
least execute the samtools command internally. But when I add the 2>&1,
galaxy can no longer find the command. Do I need to specify a path
somewhere in the galaxy-dist?
I apologize for the very long message.
Thanks in advance,
I am trying to set up MACS tool on local Galaxy. Galaxy comes with
it's macs-wrapper.py and macs-wrapper.xml, but it wants to use "macs"
not "macs14" executable.
I tried to to editing macs-wrapper.py to make it use "macs14" instead,
but some options are not the same between the two, and the tool
I would appreciate if someone could give me an advice on where I can
get "macs" executable for 64-bit Linux.
Sergei (Siarhei Manakou) Manakov
California Institute of Technology
+1 626 395 3593
I am using Galaxy API for some actions and I must say that this is indeed a really great feature with a great power.
Anyway, I am trying to write a python script that one of its goals is to remove some data libraries,
But until now, I was unable to find a way to remove data library or some of its datasets using the API or by direct call to Galaxy's code.
I found a old post that claim that this feature is not yet implemented.
1) Is this has changed since? I mean, is there a way now to clean or remove completely a data library?
2) Is there a way to use Galaxy code to remove a library? Such as a function that can be used in my script to remove this library?
Thanks in advance!
I am getting following "ValueError: too many values to unpack" from Python while trying to install a tool from toll_shed repository.
File '/Users/shantanu/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__
File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/Users/shantanu/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )
File '/Users/shantanu/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator
return func( self, trans, *args, **kwargs )
File '/Users/shantanu/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository
description, repository_clone_url, changeset_revision = repo_info_tuple
ValueError: too many values to unpack
I am using galaxy-dist revision 40f1816d6857 on Mac OS 10.7 with Python 2.7. I got the same error on CentOS 5.8 platform with Python 2.6 version for the same galaxy-dist revision. Am I missing anything in the configuration file? Any pointers? Appreciate all the help.
This tool is in the Galaxy Tool Shed
(http://wiki.g2.bx.psu.edu/Tool%20Shed) so to use for now, use with a
local/cloud instance (http://getgalaxy.org) would be the best route:
search for "cutadapt"
I will also forward this to the galaxy-dev list where tools are
discussed. Going forward, that would be the best place to make requests.
We will open a ticket at bitbucket if the team decides this would be a
good fit for the public server.
-------- Original Message --------
Date: Mon, 30 Apr 2012 13:49:53 -0500
From: Tilahun Abebe <tilahun.abebe(a)uni.edu>
To: Jennifer Jackson <jen(a)bx.psu.edu>
I want to use cutadapt to trim adapters on Galaxy main. It looks like it
is not listed under the tools. Can you add cutadapt to Galaxy?
Thanks for your help.
University of Northern Iowa
This is a question best directed to the galaxy-dev list, which I have CC'd.
On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote:
> Dear Nate,
> Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im particularly interested in running NGS tools
> like BWA, BOWTIE etc in the cluster with Torque PBS. Just wondering if galaxy is capable of parallel processing of data. 1 user running BWA in 10 cores in which 10 instances of BWA in each core parallely processing the mapping of 250 GB of reads data on to the reference genome.
> Is this possible?
The BWA tool itself supports running multithreaded, see the threads option in the wrapper. Also, Galaxy can split a tool's inputs, run a tool many times, and merge the outputs. I am not sure whether this is possible or implemented with BWA, but I would encourage you to look in to whether this would work for your needs.
> I have another issue as well. Im unable to finish FASTQ grooming of the reads of size 250GB even after 2 days of processing. Is there a way to circumvent the grooming step? or any way to make the grooming speed up?
Assuming this is on a local server, make sure you have set the config option set_metadata_externally = True. You don't need to run the groomer if your fastq file is valid fastqsanger.
> Your quick response will be really appreciated.
> Thank you
> Kiran Jaycee
> Bioinformatician, BINET
> ELOGIC Technologies Pvt. Ltd.
> #1, 2nd Floor, 100 Ft. Ring Road,
> Kathriguppe, Banashankari III Stage,
> Bangalore - 560085
> Phone : +91 (0)80 4080 3829
> Website : www.elogic.co.in
There is apparently a persistent problem with samtools which normally lives
at /usr/bin/samtools. I encountered a similar problem in Python when
uploading BAM files.
I did not resolve the problem. I hacked for a while on binary.py in a lib/
subdirectory and used os.system to send myself mail describing the
effective path at various points, and I added a missing
statement and scattered some log.WARNING statements strategically. All
this told me nothing. So I made a few symlinks to samtools. The one that
got things working was
ln -s /usr/bin/samtools /home/galaxy/bin/samtools
so--worked around but not resolved.
On Tue, Apr 17, 2012 at 12:15 PM, zhengqiu cai <caizhq2005(a)yahoo.com.cn>wrote:
> Hi All,
> I submitted a job to convert sam to bam, and the job was running forever
> without outputing the result. I then checked the log, and it read:
> Traceback (most recent call last):
> File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> line 336, in finish_job
> drm_job_state.job_wrapper.finish( stdout, stderr )
> File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 637, in finish
> dataset.set_meta( overwrite = False )
> File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py", line
> 875, in set_meta
> return self.datatype.set_meta( self, **kwd )
> File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 179, in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
> It means that the samtools is not in the PATH. I tried to set the PATH in
> a couple of methods according the Galaxy documentation:
> 1. put the path in the env.sh in the tool directory and symbolink default
> to the tool directory, e.g. default ->
> 2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request
> 3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request
> none of them worked, and I got the above same problem.
> Then I checked the job log file in the job_working_directory, and it read:
> Samtools Version: 0.1.18 (r982:295)
> SAM file converted to BAM
> which shows that sge knows the PATH of samtools. To double check it, I
> added samtools index to Galaxy, and it worked well. I am very confused why
> SGE knows the tool path but cannot run the job correctly.
> The system I am using is ubuntu on EC2. I checked out the code from
> galaxy-dist on bitbucket. Other tools such as bwa and bowtie worked well
> using the same setting method(put env.sh in the tools directory to set the
> tool path)
> Thank you very much for any help or hints.
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