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mailing list840
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Comment: C: How To Provide .Gtf File To Tophat2
... That's very helpful! Thanks. -Greg ...
written 5.2 years ago by mailing list840
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How To Provide .Gtf File To Tophat2
... I'm trying to translate this command line run into the Galaxy GUI but I'm not seeing a place to specify the .gtf file. Does anyone know? tophat2 -p 8 -G /groups/bowtie2_index/mRNA.gtf -o /groups/hp_1 /groups/genome /groups/reads.fastq thanks, Greg ...
bowtie alignment written 5.2 years ago by mailing list840 • updated 5.2 years ago by Jennifer Hillman Jackson24k
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Comment: C: Local Install - Understanding Upload File Concept
... No, I don't see anything like that in the log after I started the upload. Any ideas on how to see what might be going wrong there? -Greg ...
written 5.3 years ago by mailing list840
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Comment: C: Local Install - Understanding Upload File Concept
... Also what would I look for in the log file to know if it's issuing jobs? I started a new upload, but I don't see anything from the galaxy user when I run qstat. Thanks again. Greg ...
written 5.3 years ago by mailing list840
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Comment: C: Local Install - Understanding Upload File Concept
... I guess I'm still confused about new_file_path. The upload tool uses that directory to store files temporariliy until the upload completes? And then moves it? (Will it clean up anything placed in the new_file_path directory?) Thanks, Greg ...
written 5.3 years ago by mailing list840
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Comment: C: Local Install - Understanding Upload File Concept
... Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't verified that it's doing that yet. I wanted to upload a file to test on first. Here are the changes I made to universe_wsgi.ini after copying the sample: -Greg ...
written 5.3 years ago by mailing list840
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Local Install - Understanding Upload File Concept
... I'm confused if files are uploaded through the Galaxy server or through Apache? I already set up the Apache proxy explained here: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy (Does that affect uploads?) My goal is to let users upload as large of files as possible through HTTP. So fa ...
galaxy written 5.3 years ago by mailing list840 • updated 5.3 years ago by Nate Coraor3.1k
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Galaxy Server Configuration - What Is [Server:Main]?
... I see this setting at the top of universe_wsgi.ini: # Configuration of the internal HTTP server. [server:main] I'm confused what that's for. Do I need to change it? Thanks, Greg ...
written 5.3 years ago by mailing list840 • updated 5.3 years ago by Dannon Baker3.7k
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Comment: C: Trouble Installing Galaxy On Cluster
... So I ended up moving these lines: export DRMAA_LIBRARY_PATH=/sge/current/lib/lx-amd64/libdrmaa.so export TEMP=/scratch/galaxy source /usr/local/galaxy/galaxy_python/bin/activate from galaxy.fedora-init to the galaxy user's .bashrc file. (/home/galaxy/.bashrc) It seems to be working, I see the vir ...
written 5.3 years ago by mailing list840
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Comment: C: Trouble Installing Galaxy On Cluster
... Thanks Scott. I think I already have that call in there. That's why I'm so confused. See line 21 http://pastie.org/5351396 Is something not working with that call. Maybe that call affects root and not the galaxy user? -Greg ...
written 5.3 years ago by mailing list840

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