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_primer_clip.txt
> https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_primer_clip.xml
> https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_primer_clip.py
> 
> <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


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