Hello all,
With recent additions to lib/galaxy/util/__init__.py
I have started getting the following in the std out of bowtie and
cufflinks (and probably other tools as well):
ERROR: Unable to read builds file: [Errno 2] No such file or
directory:
'/mnt/galaxyTools/galaxy-central/lib/galaxy/uti
On Tue, Aug 21, 2012 at 4:46 PM, Ted Goldstein wrote:
> I am developing several tools that will need to read and write multiple
> data files at once. For example, Eisen Cluster produces a heatmap
> which consists of three files: a .cdt file, .atr file and a gtr file which
> are
> the underlyin
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz wrote:
> HI
>
>
> We have been struggling with this problem since we updated to
> "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the
> time to figure out whether it was a bug or whether we made a mistake.
> Unfortunately, it n
On Tue, Aug 21, 2012 at 5:36 PM, Carlos Borroto
wrote:
> Not what I was hoping for.
>
> I usually link without copying into galaxy, so it won't help me. I
> also got excited because I thought there was the possibility of
> working with fastq files without having to keep unzipped datasets,
> that w
Not what I was hoping for.
I usually link without copying into galaxy, so it won't help me. I
also got excited because I thought there was the possibility of
working with fastq files without having to keep unzipped datasets,
that would safe a lot of space, even if processing gets slower.
Hans, I
On 08/21/2012 04:23 PM, Carlos Borroto wrote:
Interesting...
Hans, could you specify what tools currently available in Galaxy
support gzip'd fastq files?
Any in this list?:
- Bowtie/Tophat
- FastQC
- FASTQ Groomer
I can't tell you, as we don't use any of these tools in Galaxy as
provided i
I just upgrade our galaxy to the latest release : 7487:be81990d148a and
ran the migration tool script for freebayes.
I received the following error:
No handlers could be found for logger "galaxy.tools"
/opt/galaxy/galaxy_dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam
On Aug 17, 2012, at 6:08 PM, Rodolfo Aramayo wrote:
> Hi,
>
> We are in the process of deploying a small Galaxy server here at Texas
> A&M University
> I am a GNU/Linux kind of guy
> My IT people want to use an SMB-mounted drive share as a backup destination
> I am concerned that this might impac
Hi Clare,
If you use the system python, or a build from python.org, you should be fine.
It's Enthought python, which is only built for a single architecture, that's
the reason for having to do so much manual egg building.
--nate
On Aug 19, 2012, at 7:36 AM, Tomithy Too wrote:
> Hi Clare,
>
This is not tool specific.
Instead, galaxy automatically unzips as files are uploaded.
beware: it only supports one data set per zipped file - so gzipped fastqs are
find.. but a tarball of a bunch of fastqs is not.
Brad
On Aug 21, 2012, at 10:23 AM, Carlos Borroto
wrote:
> Interesting...
>
Interesting...
Hans, could you specify what tools currently available in Galaxy
support gzip'd fastq files?
Any in this list?:
- Bowtie/Tophat
- FastQC
- FASTQ Groomer
Having the possibility to use these tools without needing to unzip
fastq files would be great and I didn't know you could do tha
Hi Paul
what version of Galaxy are you using? In older versions, it was
important, that there was no blanc space between the email adress'
(although, as far as IO know, this has been fixed).
Regards, Hans
On 08/21/2012 12:47 PM, Paul-Michael Agapow wrote:
A peculiar quirk – I’m configuring
On Tue, Aug 21, 2012 at 11:47 AM, Paul-Michael Agapow
wrote:
> A peculiar quirk – I’m configuring a new Galaxy system for production use
> and can’t get it to recognise my account as an admin, i.e. the admin menu
> doesn’t appear after I’ve added my email address to the admin_user line in
> the un
A peculiar quirk - I'm configuring a new Galaxy system for production use and
can't get it to recognise my account as an admin, i.e. the admin menu doesn't
appear after I've added my email address to the admin_user line in the universe
file. Of course, I've restarted the instance multiple times,
Hi all,
I'm having issues rsync'ing the reference data of Galaxy
$ rsync -avvvzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
opening tcp connection to datacache.g2.bx.psu.edu port 873
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.201.89):
Connection timed out (110)
rsync error
Hi all,
I am wondering what is the best way to dynamically update tool data files
without having to restart Galaxy.
The context is as follows. A cron job is regularly creating new blast databases
(or in general: e.g. tool data needed to fill a dropdown list). The same cron
job could be adapted s
Hello Susan
The tool is using the identifier in the "gene_id" attribute from the
reference annotation GTF to name the output.
This link at the tool manual can help:
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
The iGenomes dataset may be what you are looking for. "Shared Data ->
Data
moving to dev..
Hi Jen and Brandon
well, I don't agree (or maybe I misunderstood the question/answer):
we work a lot with compressed data (ie g'zipped fastq files from the
sequencer), and link them as a Galaxy data library. We preselect 'fastq'
as file format.
And then, the first tool
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