User: onspotproductions

Reputation:
30
Status:
New User
Location:
United States
Last seen:
5 months, 1 week ago
Joined:
1 year, 3 months ago
Email:
o****************@gmail.com

Posts by onspotproductions

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Genomes no longer available after database migration
... When I migrated the galaxy it appears to have changed the location of the .loc files which identify the genomes. They were no longer in tool-data, but had moved to another location. I modified those and was able to add the genomes. ...
written 5 months ago by onspotproductions30
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Setting up SLURM DrMMA for galaxy
... I am building a computing cluster for use with galaxy and have setup SLURm as the resource manager. I know the drmaa addon is necessary but am unsure the best way to compile it for use with galaxy. I found this guide and am curious as to any settings I may need to change before compiling. http://gm ...
slurm galaxy cluster rna-seq written 5 months ago by onspotproductions30
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Genomes no longer available after database migration
... I recently moved out production galaxy from one postgres database to another. In the process I can no longer access the custom genomes added in our tophat .loc file. I attmepted to reload the file using local data however it is not seeing the genome indices. ...
index database galaxy genome admin written 5 months ago by onspotproductions30 • updated 5 months ago by Jennifer Hillman Jackson21k
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Comment: C: Integrating Pre-built Bowtie2 Indexes
... Thank you, that is exactly the information I needed. ...
written 5 months ago by onspotproductions30
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Integrating Pre-built Bowtie2 Indexes
... I have obtained the pre-built bowtie2 indexes from Ensemble and would like to integrate them into our galaxy install to be used with tophat2. What is the best method to add these builds and have them correctly identified by the tools. ...
bowtie2 galaxy bowtie rna-seq written 5 months ago by onspotproductions30 • updated 5 months ago by Devon Ryan1.3k
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Comment: C: HTCondor & galaxy setup guide
... I understand the config portion for galaxy. I am primarily looking for a guide to getting HTCondor running properly and cannot quite follow the provided manual instructions. I am looking for a guide that also includes the galaxy portion or the best way to setup the galaxy cluster using HTCondor. ...
written 5 months ago by onspotproductions30
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Galaxy Local Instance, Docker & Coreos cluster
... I am curious to see if anyone has developed a compute cluster using etcd on coreos and the galaxy docker container? I am attempting to setup a cluster currently using HTCondor, but would like to see if this approach would be more practical. ...
coreos galaxydocker docker galaxy written 5 months ago by onspotproductions30
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HTCondor & galaxy setup guide
... I am looking for a descriptive tutorial on setting up a galaxy environment using htcondor as the DRM. I have looked at the guides but am slightly lost. Any information would be highly appreciated. ...
galaxy htcondor condor cluster rna-seq written 6 months ago by onspotproductions30 • updated 6 months ago by nitesh.turaga100
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Comment: C: switch between cloudman and local - use condor?
... One thing I should have mentioned is that all machines require mounting of the same NFS and there are some limitations when it comes to using NFS. You may want to look into NFSv4 to do this. ...
written 6 months ago by onspotproductions30
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Issue with running TOphat 2 on local galaxy with Rsync genomes
... I attempted to run a test job on our new local galaxy instance and generated an error when attempting to align RNA reads to HG19 using tophat 2. I have never encountered this issue before. Traceback (most recent call last): File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/runners ...
rna-seq galaxy assembly written 6 months ago by onspotproductions30

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