Hi,
Just add some info about this, I have attempted to do so on SGE cluster.
I found that $NSLOTS works only for MPI jobs as it's part of the MPI
integration in SGE.
Other non MPI jobs won't work. For example:
python parallel_groomer.py input output $NSLOTS, $NSLOTS won't be replaced
by the SGE
I have a situation I'm sure others have faced but I can't see how to solve it
without hacking the src and I'd rather not do that just yet as it complicates
upgrades.
We're using Apache with NTLM and "require valid user" so it's a corporate
domain and only authorized users are allowed access.
If
The picard based tools nicely infer a reference sequence, and still allow the
user to override.
However, this inference does not work in a workflow, since that select list has
no value.
I'm trying to come up with a clean way for the workflow logic to read the input
dataset dbkeys, but I'm not
On Mon, Jul 16, 2012 at 6:10 PM, Espin, Almudena
wrote:
>
> Hi guys,
> I am writing a wrapper for makeblastdb. The problem is that
> Galaxy doesn’t support the blastdb data format, so this has
> to be added if a makeblastdb wrapper is to work properly.
> I have problems modifying the registry.py,
Hi Irene,
You likely saw the reply, but for everyone else:
http://user.list.galaxyproject.org/cufflinks-reference-annotation-td4654251.html
Next time, posting to a single list is best. For questions like this
one, galaxy-user is appropriate. Galaxy-dev is generally used for
development topics.
Hi guys,
I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t
support the blastdb data format, so this has to be added if a makeblastdb
wrapper is to work properly.
I have problems modifying the registry.py, Could anyone specify which changes
have to be done?
Thank you
Sorry, that's all I have. Le-Shin
On Jul 15, 2012, at 4:41 AM, Morris Chukhman wrote:
> Yes! That seems to have worked! Thank you very much, Le-Shin!
>
> Are there any more of these dependencies that require these little "patches"
> to build and install properly?
>
> Morris
>
> On 7/14/201
Hello,
I want to know if I can do something on galaxy. I have a folder for the
chromosome 1 with start of G4 and start of ORI. For each start G4 I associated
all of start ORI. For example if I have 2 start G4 (2 lines) and 4 start ORI (2
lines), I will have on a new file 8 lines.
startG4
Hi guys,
I'm new wth NGS and have few basic questions about Galaxy for RNAseq:
1. when I run Cufflinks on my TopHat accepted hits, WHEN and WHY do i have to
chose a reference annotation?Results are obviously different
2.if i chose this option, which one of the 2 references I have to upload from
U
Dear Galaxy community,
I have a problem with uploading data on Galaxy, using the get data/upload file
tool, and I can't figure out where the trouble comes from.
Basically, when I try to upload files (size ranging from less than 1 Mo up to
600 Mo), sometimes it works, sometimes it doesn't (kee
Hello,
I have added a tool in my local instance to map BAM files on reference
genome fasta file thanks to BWA.
This tool runs, and the output file generated in database/files/000 is
correct (not empty and good data inside) but the output listed in the
history panel of Galaxy interface , is em
Hi,
We have set up a local instance of galaxy-dist, using pbs-python to
communicate with our HPC. Everything is working great, except for the
upload functionality.
When I assign the upload1 to local:/// , uploading of small files
through the web-site works, and upload of large files by ftp w
Hi Nate,
thanks a lot for your hints. I was finally able to fix the problem. Galaxy
couldn?t find the .drmerr file because our
SGE installation merged .drmerr into .drmout... now everything works fine!
Cheers,
Sascha
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