User: Peter Cock

gravatar for Peter Cock
Peter Cock1.4k
Reputation:
1,410
Status:
Trusted
Location:
European Union
Website:
http://blastedbio.blog...
Scholar ID:
Google Scholar Page
Last seen:
1 year, 4 months ago
Joined:
6 years, 10 months ago
Email:
p*********@googlemail.com

I contribute to a number of open source bioinformatics projects, including Biopython and Galaxy. I have written a number of Galaxy tools & wrappers, co-ordinate the Galaxy BLAST+ wrappers, and currently serve on the Intergalactic Utilities Commission (aka the Galaxy ToolShed Police).

Posts by Peter Cock

<prev • 150 results • page 1 of 15 • next >
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How to reset a user's password at the command line?
... When a Galaxy server doesn't have email setup, users cannot use the "reset password" functionality. It is possible for any of the Galaxy administrators to log in, and goto the "Admin" tab, then on the left hand pane under "User Management", "Users", reset user passwords. Is resetting a user's passw ...
password galaxy admin written 19 months ago by Peter Cock1.4k
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Comment: C: Biopython as repo dependency
... Yep. When developing tools and packages I try to do everything on the public TestToolShed before the (main) ToolShed, which generally works since the dev-team and IUC core packages are on both. ...
written 3.1 years ago by Peter Cock1.4k
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Comment: C: Error executing Bowtie2: bam_index_build2() not yet implemented
... Known bug in samtools, see https://github.com/samtools/samtools/issues/199 ...
written 3.1 years ago by Peter Cock1.4k
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Comment: C: Error after upload bam file
... See also later duplicate question https://biostar.usegalaxy.org/p/9335/ ...
written 3.1 years ago by Peter Cock1.4k
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Comment: C: Error executing Bowtie2: bam_index_build2() not yet implemented
... Duplicate of https://biostar.usegalaxy.org/p/7928/ ...
written 3.1 years ago by Peter Cock1.4k
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Comment: C: how solve this error Error executing tool: No dataset upload groups were found.
... See https://biostar.usegalaxy.org/p/7928/ for this problem (a bug in samtools) ...
written 3.1 years ago by Peter Cock1.4k
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Comment: C: Error after upload bam file
... Yes, I get the same error Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented from samtools v1.1. It is a known bug, see https://github.com/samtools/samtools/issues/199 - I am looking at a hack to work around this: https://github.com/peterjc/picobio/blob/master/sa ...
written 3.1 years ago by Peter Cock1.4k
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Answer: A: fastq data types
... See http://dx.doi.org/10.1093/nar/gkp1137 fastqcssanger = FASTQ color space using Sanger encoding (PHRED scores + 33) fastqillumina = FASTQ using now obsolete Illumina encoding (PHRED scores + 64) fastqsanger = FASTQ using Sanger encoding (PHRED scores + 33), probably you want this fastqsolexa ...
written 3.3 years ago by Peter Cock1.4k
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Comment: C: Proposed IRC Channel Logging Policy Change
... Perfect :-) ...
written 3.3 years ago by Peter Cock1.4k
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Answer: A: Proposed IRC Channel Logging Policy Change
... I have no idea how easy this is, but I would suggest having an official IRC bot periodically post on the channel reminding people that the chats are being logged and include the archive URL. Maybe hourly in the first couple of weeks, then reduce this to every few hours (so that regardless of which ...
written 3.3 years ago by Peter Cock1.4k

Latest awards to Peter Cock

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Nucleotide Analysis - Gc Percentage
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: fastq data types
Scholar 3.3 years ago, created an answer that has been accepted. For A: fastq data types
Scholar 3.5 years ago, created an answer that has been accepted. For A: Adding custom tools: resolving (external ) XML entities
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Adding custom tools: resolving (external ) XML entities
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.8 years ago, created 100 posts.

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