A colleague has asked me to set up a galaxy server for purpose of running
tophat/cufflinks.
A recent paper in BMC Genomics would indicate that those tools are integrated
into Galaxy.
When I download (hg clone) the distribution, I only see tophat, but none of the
other tuxedo software. The funn
I am a total galaxy newbie who is setting up a galaxy server for a group of
internal researchers in order to do RNASeq analysis.
I can see where I can upload libraries from the galaxy server, but I can’t
figure out how to load the “available” data (fastqs) — to clarify instead of
asking users t
Hi all,
I have been trying to set up my galaxy instance to use SGE -- I created a
job_conf.xml using the sample as a model and updated the galaxy user bashrc
with the DRMAA_LIBRARY_PATH
export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so
But when I try to add data to a library I get
mp;m=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0A&s=9978e8d2a1f01560f249e5439efff9f047338fa4fab2a1be17e5499555f224a9>
On 21/01/2014 22:16, Cantarel, Brandi L. wrote:
Hi all,
I have been trying to set up my galaxy instance to use SGE -- I created a
job_conf.xml using the sample as a model and updated the galaxy user bashrc
with th
xample.
-b n
Thomas
On 22/01/2014 16:02, Cantarel, Brandi L. wrote:
Are you asking if I can submit jobs to sge with the galaxy user on the server —
yes, I can, at least I can on the command line...
On Jan 22, 2014, at 3:00 AM, Thomas Bell
Hi all,
I am trying to set up my own galaxy server (and I don't know much IT) and
thought that I had my sge working properly, but when I try to load data -- via
manage data libraries on the web interface, I get the following error:
/bin/sh: module: line 1: syntax error: unexpected end of file
/b
Hi,
I am testing my newly installed galaxy instance. When I try to use a simple
tool like fastq_to_fasta, I get the following error:
UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in
position 693: ordinal not in range(256)
Anyone know how I can fix this?
Thanks!
Brandi
