User: chaoyuan

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chaoyuan80
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Posts by chaoyuan

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How to get / create GFF files for Cufflinks for Zebra Finch genome (taeGut2) on Galaxy ?
... Hi, I'm trying to perform Cufflink on my local instance of Galaxy. I've installed taeGut2 genome from UCSC. I'm having trouble with the GFF files needed for Cufflink, though. I know that I can create a GFF file using the UCSC table browser. However, there are numerous options and I'm very confu ...
cufflinks galaxy annotation gff written 13 months ago by chaoyuan80 • updated 13 months ago by Mo Heydarian790
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Answer: A: Reference Genomes do not exist in local Galaxy's Bowtie2
... You can fetch genome using the tool data_manager_fetch_genome_all_fasta . After you find this tool in the tool shed and install to the local Galaxy instance, go to Admin -> Data -> Local Data . Then under Run Data Manager Tools, you'll see Reference Genome. You can then use it to download geno ...
written 19 months ago by chaoyuan80
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Answer: A: Unable to finish job for both RNA-STAR and tophat2
... Ok. I think I finally understood this. The samtools that's called by binary.py when converting SAM file to BAM file is independent from the samtools installed as dependency by other repository tools. It occurred to me when I monitor the task with top : tophat is using samtools 0.1.18, which I di ...
written 19 months ago by chaoyuan80
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Unable to finish job for both RNA-STAR and tophat2
... This is the problem I keep running into with both Tophat and RNA-Star on my locally installed Galaxy. They both cannot finish the job and save me the following error message: Traceback (most recent call last): File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/runners/local.py", line 128, in ...
samtools galaxy config admin tophat written 19 months ago by chaoyuan80 • updated 19 months ago by Jennifer Hillman Jackson23k
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Answer: A: How to add reference annotation for Cufflinks to local Galaxy?
... It appears that Cufflinks takes GFF3 files but not GTF files. I ended up downloading GFF3 files from [enter link description here][1] through Admin -> Data -> Data libraries. If access restriction is not set, it's available to all the users. From Shared Data -> Data Libraries, the reference ...
written 19 months ago by chaoyuan80
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Comment: C: how to do tophat
... What is the error in your tophat results? ...
written 19 months ago by chaoyuan80
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Answer: A: RNA STAR unable to finish job
... I did two things and I think the problem is gone 1. Instead of downloading source codes as zip file from the galaxy github repository, I used git clone. 2. I installed virtualenv. I guess these are just what should be done if one wishes to install a local Galaxy instance. It's really difficult ...
written 19 months ago by chaoyuan80
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How to add reference annotation for Cufflinks to local Galaxy?
... I'm interested in using Cufflinks with reference annotation on my local Galaxy instance. I'm wondering how I can install reference annotation to my local Galaxy so that it's available to all the user? I tried searching for data_manager in the tool shed but I don't see such tool for fetching referenc ...
galaxy cufflinks written 19 months ago by chaoyuan80
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Comment: C: RNA STAR unable to finish job
... Thanks for the reply. I installed the tools with managed dependencies. That is, when I select the tool and click 'Install to Galaxy', I leave the 'Handle repository dependencies' and 'Handle tool dependencies' checked. In the tool dependency directory, I see that binaries for all the tool dependenci ...
written 20 months ago by chaoyuan80
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Comment: C: RNA STAR unable to finish job
... If I do that, I'll find the samtools found by the system to be the version where the env.sh is located. I checked the env.sh, it's recording correctly the path to the samtools. That's whey I suspect it's not sourced by Galaxy before a job runs. Otherwise, samtools would have been found correctly. ...
written 20 months ago by chaoyuan80

Latest awards to chaoyuan

Scholar 19 months ago, created an answer that has been accepted. For A: Error installing tool dependency ncurses version 5.9
Scholar 20 months ago, created an answer that has been accepted. For A: Bowtie2 error on locally installed Galaxy : unable to finish job
Scholar 21 months ago, created an answer that has been accepted. For A: Bowtie2 error on locally installed Galaxy : unable to finish job

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