User: 18Kbeyond

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18Kbeyond20
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New York
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2 months, 3 weeks ago
Joined:
10 months, 2 weeks ago
Email:
y*****@columbia.edu

Posts by 18Kbeyond

<prev • 29 results • page 1 of 3 • next >
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How do I release documentation? -- Publishing tools to the Main ToolShed
... I have added our own scripts for analyzing CLIP data to http://intron.c2b2.columbia.edu:8888/ This galaxy instance is customized and maintained by Chaolin Zhang lab. It is based on the system developed by The Galaxy Project. Is there a detailed description on how to push them to Galaxy so everyone ...
galaxy gtn publish toolshed planemo written 12 weeks ago by 18Kbeyond20 • updated 12 weeks ago by Jennifer Hillman Jackson25k
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Comment: C: where to find cutadapt tool version / where to find the lastest tool
... Thank you for the advice. For now I would like to stick to the same tool (Cutadapt). The reason I asked for Galaxy's Cutadapt version is because I need to use Cutadapt before some downstream analysis --- I am trying to run Galaxy version as well as command line version, and comparing the results t ...
written 5 months ago by 18Kbeyond20
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where to find cutadapt tool version / where to find the lastest tool
... Hi. When I searched for "cutadapt" here https://toolshed.g2.bx.psu.edu/ I see one result that "Installable Revision" is 2015-05-26. There are 3 results but the other two seem wrong - their "type" is "Tool dependency definition" and their revision dates are older. The problem is, https://cutadapt.r ...
trimmomatic version trim trim-galore cutadapt written 5 months ago by 18Kbeyond20 • updated 5 months ago by Jennifer Hillman Jackson25k
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Answer: A: Can I submit the next step when this step is still processing (yellow)
... Found it here https://galaxyproject.org/learn/advanced-workflow/extract/ Thanks guys! ...
written 6 months ago by 18Kbeyond20
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Can I submit the next step when this step is still processing (yellow)
... Hi. Is it safe to submit the next step B whose input is the output of A when this step A is still processing (file in yellow) or even waiting (file in grey)? I want to do this because I want to submit jobs all in once so that galaxy can automatically starts the next step B when A is finished, so t ...
workflow yellow written 6 months ago by 18Kbeyond20
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Comment: C: awk ... fatal: print to "standard output" failed
... Hi Jen, So I replaced gunzip -c with cat for galaxy script as galaxy seems to convert fastq.gz to fastq. However, after I remove / in front of 0 and 1, I still got error message: awk: (FILENAME=- FNR=613) fatal: print to "standard output" failed (Broken pipe) cat: write error: Broken pipe ...
written 9 months ago by 18Kbeyond20
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Comment: C: awk ... fatal: print to "standard output" failed
... Thank you very much for your helpful reply as always! ...
written 9 months ago by 18Kbeyond20
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awk ... fatal: print to "standard output" failed
... Hi. I uploaded the fastq.gz file below to galaxy. I noticed that galaxy will convert it to fastq, so I didn't include gunzip before awk. (the code works in command line) (I have tried adding gunzip -c before awk, like I do in command line, but galaxy will say "gzip: ...dat: not in gzip format ) wg ...
syntax galaxy awk tool written 9 months ago by 18Kbeyond20 • updated 9 months ago by Jennifer Hillman Jackson25k
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Comment: C: Is it possible to auto-detect the database/genome of the input file?
... Thank you very much. My hope is not about letting some tool help select genome completely so that I don't need to have those 4 lines. I still want the the user to see the drop-down box and select a genome. My hope is that the default genome will be changed to the genome of the input file. Say if th ...
written 9 months ago by 18Kbeyond20
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How to specify output format by a drop-down box?
... Hi. How to let the user select from a drop-down box for the desired output format (formatA or formatB) and galaxy can output the file with selected format? ...
output format written 9 months ago by 18Kbeyond20 • updated 9 months ago by Jennifer Hillman Jackson25k

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