User: chaoyuan

gravatar for chaoyuan
chaoyuan80
Reputation:
80
Status:
Trusted
Location:
Last seen:
1 year, 11 months ago
Joined:
2 years, 8 months ago
Email:
c*******@yahoo.com

Posts by chaoyuan

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
956
views
1
answer
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 2.0 years ago by chaoyuan80 • updated 2.0 years ago by Mo Heydarian830
0
votes
1
answer
994
views
1
answers
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 2.6 years ago by chaoyuan80
0
votes
1
answer
855
views
1
answers
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 2.6 years ago by chaoyuan80
1
vote
1
answer
855
views
1
answer
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 2.6 years ago by chaoyuan80 • updated 2.6 years ago by Jennifer Hillman Jackson25k
1
vote
1
answer
825
views
1
answers
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 2.6 years ago by chaoyuan80
1
vote
1
answer
661
views
1
answers
Comment: C: how to do tophat
... What is the error in your tophat results? ...
written 2.6 years ago by chaoyuan80
2
votes
3
answers
959
views
3
answers
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 2.6 years ago by chaoyuan80
1
vote
1
answer
825
views
1
answer
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 2.6 years ago by chaoyuan80
0
votes
3
answers
959
views
3
answers
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 2.6 years ago by chaoyuan80
0
votes
3
answers
959
views
3
answers
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 2.6 years ago by chaoyuan80

Latest awards to chaoyuan

Scholar 2.6 years ago, created an answer that has been accepted. For A: Error installing tool dependency ncurses version 5.9
Scholar 2.6 years ago, created an answer that has been accepted. For A: Bowtie2 error on locally installed Galaxy : unable to finish job
Scholar 2.7 years ago, created an answer that has been accepted. For A: Bowtie2 error on locally installed Galaxy : unable to finish job

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour