User: gb

gravatar for gb
gb30
Reputation:
30
Status:
New User
Location:
Last seen:
8 hours ago
Joined:
2 weeks, 6 days ago
Email:
m**************@gmail.com

Posts by gb

<prev • 6 results • page 1 of 1 • next >
0
votes
0
answers
76
views
0
answers
Comment: C: FASTA sequences not blasting.
... I am not familiar with the public servers so I can not help you more. But you need to mention which galaxy server you are using. Also check the input, before you can blast against a reference you need to index the reference fasta file. So basicly you convert a fasta file to a blast database. EDIT ...
written 10 days ago by gb30
0
votes
0
answers
76
views
0
answers
Comment: C: FASTA sequences not blasting.
... Not sure what you mean but this is already wrong: > My FASTA sequences ( in tabular format) are not blasting Fasta is a certain format, first you have a line starting with ">" and a description and the next line is a sequence. https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Bl ...
written 12 days ago by gb30
0
votes
1
answer
85
views
1
answers
Answer: C: Python outputs empty on history
... So you pass the variable $output1 from the xml file into your python script. The variable $output1 is basically just a path, a output location. So for example this: with open(filename, 'w') as f: f.write(content) The filename should be the $output1 value. ...
written 14 days ago by gb30
0
votes
1
answer
85
views
1
answers
Comment: C: Python outputs empty on history
... I never used "from_work_dir" so not sure about that. Maybe it needs to be the full path. I would use $output1 as parameter for the python script. So: python '$__tool_directory__/LungCARD_report.py' "$patientID" "$sampleID" "$birthday" "$gender" "$labKit" "$sequencer" "$vcf_file" "$idxstats" "$ ...
written 17 days ago by gb30
0
votes
1
answer
79
views
1
answers
Comment: C: Can't import pandas with python script
... Also realize that you need to restart galaxy every time when you make a change to a xml file. Your problem is solved now but if you are installing a python package in the venv of galaxy you see the installation progress when you start galaxy the first time after you added it. So if you do not see th ...
written 19 days ago by gb30
3
votes
1
answer
79
views
1
answers
Answer: A: Can't import pandas with python script
... Galaxy executes the python scripts in a virtual environment. So it uses the packages that are installed there and not the ones on your machine. I think you need to add a requirement https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#dependency-resolvers. You can also not use th ...
written 20 days ago by gb30

Latest awards to gb

Scholar 20 days ago, created an answer that has been accepted. For A: Can't import pandas with python script
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Can't import pandas with python script

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour