John, I'll take a look at the program. There isn't a great way to do
this until the dependency installation system is working. A thin
python wrapper (using Cython) would be the usual trick we would use.
However: have you considered just using cat? This should be completely
valid for gzip
Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE,
for e.g. the workflow editor works now works and the history expand/collapse
works! :)
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On Wed, May 18, 2011 at 6:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Kanwei,
Could you merge this branch or transplant this fix please?
https://bitbucket.org/peterjc/galaxy-central/changeset/3c0b903c86a9
https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_05_18
New
Hi All,
I have some problem with extension of file.some executables file will
recognize the only the specific extension like autodock . it takes one
input file ( extension with .dpf ) and one outpt file (extension with
.dlg). how can we resolve such type of problem .
Regards
Shashi
Sorry, it slipped by. Committed!
On Wed, May 25, 2011 at 12:48 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Wed, May 18, 2011 at 6:40 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Kanwei,
Could you merge this branch or transplant this fix please?
Thank YOU for reporting them ;)
On Wed, May 25, 2011 at 11:33 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE,
for e.g. the workflow editor works now works and the history expand/collapse
works! :)
Hi Shashi,
You can add your own datatypes using the instructions here:
https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes
Thanks,
K
On Wed, May 25, 2011 at 1:05 PM, shashi shekhar meshash...@gmail.comwrote:
Hi All,
I have some problem with extension of file.some executables
Shashi,
All of Galaxy's datasets have the extension .dat so your problem is
not uncommon. The general solution to this is to create temp files
that have the the required extensions for the tool and point them to/
from the actual Galaxy input and output. There are several ways to do
this.
On Wed, May 25, 2011 at 1:10 PM, Kanwei Li kan...@gmail.com wrote:
Sorry, it slipped by. Committed!
No problem - thank you,
Peter
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Shantanu Pavgi wrote:
On May 24, 2011, at 4:49 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
I am looking at options to configure settings such as wall-time, memory,
and number of cores etc. for each tool and wondering if this can be done
using multiple cluster job runner
Shantanu Pavgi wrote:
On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote:
I have configured custom cluster_files_directory in universe_wsgi.ini file.
The cluster jobs are running fine, however job scripts, stdout and stderr
are being written in default database/pbs location. Am I
I had considered cat, but from what I have read, not all readers understand it,
or understand it as a single compressed stream. Since the resulting file would
differ from a block gzipped file (embedded gzip headers with filenames,
embedded per-file trailers, and the final CRC/size not matching
Hi, I've installed galaxy locally on my Mac, I've got everything running
fine except Bowtie/Tophat/etc. indexes.
I tried following the steps here:
https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
So my bowtie_indices.loc file looks like this:
e_coli
Sounds like we'll have to do a phased solution. I'll see if cat works well
enough for tool interoperability for now and see what we can do to make it
better (if needed) later.
Thanks, guys!
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel:
We'd like to be able to associate fixed things (project, Sample, sequencer
used) with user's FASTQ files, and we'd also like to allow users to associate
dynamic, site-specific stuff with the sequencing run. Currently, users track
their runs using a CSV sample sheet, and often they add columns
Greg.
We do not use the template_cache_path in our config. I deleted all the
files in ~/database/compiled_templates and restarted my server. I still get
the error (even with a shift reload of my browser). I've tried it (on the
Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
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