On Thu, Nov 14, 2013 at 4:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
Good news, the BLAST+ tests appear to have all passed on the Test Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb
...
Over on the main Tool Shed, the binary
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
On Thu, Apr 25, 2013 at 9:36 AM, Peter Cock wrote:
...
As noted in my last email, for some reason when running the test case,
the input FASTA file is being included on the command line TWICE.
Curiously the -hash_index argument has been
Peter,
It turns out there were two problems. First, the test environment was
not resolving the upload tool's dependency on samtools, which I've now
corrected. Second, the bam file detection on upload was broken due to
the bug in python 2.7.4's gzip module, which I've also corrected.
I have
Hi Nikhil,
Many things other than this variable number of outputs mechanism use
the new_file_path and Galaxy doesn't really manage/clean anything
put in that directory - it should be thought of as temp space (like
/tmp) but that should be shared over the cluster (if you have one).
For this
On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
It turns out there were two problems. First, the test environment was not
resolving the upload tool's dependency on samtools, which I've now
corrected.
Excellent.
On a closely related point, I understand Galaxy
On Mon, Nov 18, 2013 at 3:31 PM, Eric Kuyt erick...@gmail.com wrote:
Hi Peter,
After installing the clc testing galaxy wrapper I noticed there are still
some static paths in the wrapper.
I'm in favor of expecting binaries in the system path, but maybe that's a
matter of taste.
Yes - while
On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
With these change, I was able to write working functional tests for
your tool using the template you outlined in the Trello card. ...
I discovered no problems with
Just the licence server was installed and not the actual genomics
workbench, so I couldn't do real testing yet.
I am now downloading 6-5-1 64bit.
I'll keep you noticed.
On 18 November 2013 16:37, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Nov 18, 2013 at 3:31 PM, Eric Kuyt
Hi Peter,
On Nov 18, 2013, at 10:33 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
It turns out there were two problems. First, the test environment was not
resolving the upload tool's dependency on samtools,
On Mon, Nov 18, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
With these change, I was able to write working functional tests for
your tool using
On Mon, Nov 18, 2013 at 4:02 PM, John Chilton chil...@msi.umn.edu wrote:
On Mon, Nov 18, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
With these
Hi Peter, it turns out we only have a workbench licence, the clc_assembler
packaged with the workbench is called ./clc_assembler_ilo
which has the man page below, do you think this is the same binary as
the clc-assembly-cell assembler?
I will just try to link clc_assembler_ilo to my path and see
Hi Greg,
On Mon, Nov 18, 2013 at 4:02 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Nov 18, 2013, at 10:33 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On a closely related point, I understand Galaxy likes to store all
BAM files co-ordinate sorted and indexed - when a tool produces
a BAM
On Mon, Nov 18, 2013 at 4:23 PM, Eric Kuyt eric.ku...@wur.nl wrote:
Hi Peter, it turns out we only have a workbench licence, the clc_assembler
packaged with the workbench is called ./clc_assembler_ilo
which has the man page below, do you think this is the same binary as the
clc-assembly-cell
Hi Peter,
After installing the clc testing galaxy wrapper I noticed there are still
some static paths in the wrapper.
I'm in favor of expecting binaries in the system path, but maybe that's a
matter of taste.
Greets,
Eric Kuijt
On 30 October 2013 17:03, Peter Cock p.j.a.c...@googlemail.com
Hi,
We're using Galaxy Cloud - New Cloud Cluster to create instances of Galaxy for
training on Wednesday 20 November.
When we try to view a bam file using Trackster, we get the following error:
/opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools:
command not found
This may be due to an incorrect reference to '/mnt/galaxyTools' in the
galaxy user's .sge_request file.
If you're comfortable with ssh and editing files on the server, you can log
in and edit the file (the path should be /mnt/galaxy instead), and you
should be good to go. Feel free to reply
On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi All,
I‘m seeing some weird error messages...I googled but didn't see anything
useful:
So, it is during the wigToBigwig conversion:
Dataset generation errors
Dataset 47: Wig/BedGraph-to-bigWig on data 43
Tool
I believe subsequent jobs should use the new paths automatically, yes.
On Mon, Nov 18, 2013 at 12:14 PM, Young, Lynn (NIH/OD/ORS) [E]
ly...@mail.nih.gov wrote:
Hi Dannon,
I edited the file.
Will the system automatically recognize the change?
Warmly,
Lynn
From: Dannon Baker
Hi Dannon,
I edited the file.
Will the system automatically recognize the change?
Warmly,
Lynn
From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com
Date: Monday, November 18, 2013 1:06 PM
To: Lynn Young ly...@mail.nih.govmailto:ly...@mail.nih.gov
Cc:
Dear all,
Today I installed the SSL module for our local Galaxy instance and the
https://; link is working fine. I added this
Location /
RequestHeader set X-URL-SCHEME https
/Location
in our Apache configuration file as instructed in this webpage:
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