User: n.goue

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n.goue50
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Posts by n.goue

<prev • 21 results • page 1 of 3 • next >
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planemo shed_create lead to bioblend error 404
... Hi, I am running a dev galaxy18.01 on cluster HPC with a local toolshed. I am stopped at shed creation. My last command is `planemo shed_create --shed_target http://XXX.XXX.XX.XX:9009` > bioblend ERROR: GET: error 404: ' Not Found The resource could not be found. No route for /api/repositori ...
planemo written 3 months ago by n.goue50
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Answer: A: my tools don't locate module install by conda in mulled environement
... Hi, One possible solution is to update the first line in the perl script by replacing `#!/usr/bin/perl` by `#!/usr/bin/env perl` Check here for best practices : https://github.com/bgruening/coding_for_big_data Cheers, ...
written 4 months ago by n.goue50
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Answer: A: Error in DESeq2
... Hi, There is a nice tutorial to help you with HTseq and DeSeq2 you might know about ? http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html Good luck! ...
written 7 months ago by n.goue50
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Comment: C: cleanup_dataset doesn't free space
... Hi, actually it did some free space, 2Mb, But log said Purged 137 datasets Freed disk space: 2446911937 Elapsed time: 25.5015599728 Nothing compared... Would you have other hints ? Thanks, N. ...
written 12 months ago by n.goue50
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Answer: A: cleanup_dataset doesn't free space
... Hi Nate, I tried relative and absolute paths with the same result. If I do `df -h` before and after running the script (outside my CRON), no space is freed. Talking about `file_path`, I didn't modified it, and the default one in my config/galaxy.ini is `#file_path = database/files`. What is the bes ...
written 12 months ago by n.goue50
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cleanup_dataset doesn't free space
... Hi, I set up a CRON to handle cleaning on our local Galaxy 17.05 server. xxx/galaxy/config/galaxy.ini -d 10 -r -1 xxx/galaxy/config/galaxy.ini -d 10 -r -2 xxx/galaxy/config/galaxy.ini -d 10 -r -3 xxx/galaxy/config/galaxy.ini -d 10 -r -4 xxx/galaxy/config/galaxy.ini -d 10 -r -5 ...
galaxy administration written 12 months ago by n.goue50
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Comment: A: Error with htseq-count
... Did you solve that issue? Cheers ...
written 12 months ago by n.goue50
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Comment: C: build-in custom genomes
... Hi, I did a git diff on my folders, but nothing special pop-up. Cheers. ...
written 12 months ago by n.goue50
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Answer: A: build-in custom genomes
... Dear Jen, Thank you for your reply. I updated the dbkeys.loc, didn't modified the alignseq.loc (as I don't use it) and all_fasta.loc file looks good. The restart didn't change anything. Finally, I came back to the data manager and solved the problem by installing the package : data_manager_fetch_ge ...
written 12 months ago by n.goue50
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build-in custom genomes
... Hi, I am facing problem to make reference genome index available in mapper tools such as BWA, bowtie2 and HiSAT2. Here is what I did: - upload my genome.fasta file - build an index both localized in /data/index/bwa_index, /data/index/bowtie2_index and /data/index/hisat2_index - I modified th ...
galaxy rna-seq written 12 months ago by n.goue50

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Scholar 4 months ago, created an answer that has been accepted. For A: my tools don't locate module install by conda in mulled environement

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