Missing from tool shed - lost in migration or never uploaded?
Hi Greg, Is there anything left of the old (pre-hg) Tool Shed? I'm wondering if I ever uploaded this tool back in early 2011, in which case could it have got lost in the migration to the current hg-based Tool Shed?: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.7"> <description>Trim off 5' or 3' primers</description> <command interpreter="python"> seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file </command> ... If searching the archives is a hassle, don't worry - I'm just curious. Another likely explanation is simply that I never upload the tool - it was written for a Roche 454 dataset (to remove SMART primers) and could work directly on the SFF files. Unfortunately it is probably too slow to use on large Illumina FASTQ files. I might as well (re)post it to the Tool Shed now, perhaps with a warning that it is intended for smaller Roche/IonTorrent/Sanger sized datasets. Thanks, Peter
Hi Peter, Everything that was in the pre-hg tool shed was moved to the new tool shed - I don't remember any issues during that transition that would have eliminated anything. I don't think there is anything retrievable from the original tool shed at this point without some effort. You most likely had not uploaded this tool to the original tool shed. In any case, it's probably best to just upload it to a new repository in the tool shed. Thanks! Greg Von Kuster On Mar 28, 2013, at 10:39 AM, Peter Cock wrote:
Hi Greg,
Is there anything left of the old (pre-hg) Tool Shed? I'm wondering if I ever uploaded this tool back in early 2011, in which case could it have got lost in the migration to the current hg-based Tool Shed?:
https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri...
<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.7"> <description>Trim off 5' or 3' primers</description> <command interpreter="python"> seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file </command> ...
If searching the archives is a hassle, don't worry - I'm just curious.
Another likely explanation is simply that I never upload the tool - it was written for a Roche 454 dataset (to remove SMART primers) and could work directly on the SFF files. Unfortunately it is probably too slow to use on large Illumina FASTQ files.
I might as well (re)post it to the Tool Shed now, perhaps with a warning that it is intended for smaller Roche/IonTorrent/Sanger sized datasets.
Thanks,
Peter
On Thu, Mar 28, 2013 at 2:49 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
Everything that was in the pre-hg tool shed was moved to the new tool shed - I don't remember any issues during that transition that would have eliminated anything. I don't think there is anything retrievable from the original tool shed at this point without some effort. You most likely had not uploaded this tool to the original tool shed. In any case, it's probably best to just upload it to a new repository in the tool shed.
Thanks!
Greg Von Kuster
OK - thanks. Peter P.S. There was another possibly missing tool which prompted me to ask, Konrad's psortb wrapper (which with his blessing I am adopting, & plan to add to http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp later), which I thought I'd originally download via the old Tool Shed.
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Greg Von Kuster -
Peter Cock