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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
