Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: loops in Galaxy workflow?
1
gravatar for Daniel Elleder
4.5 years ago by
Daniel Elleder • 30
Czech Republic
Daniel Elleder • 30 wrote:

Is it possible to use loops (or cycles) in Galaxy workflow? I have a file with multiple fasta sequences and I need to process them one-by-one with a Galaxy tool (e.g. EMBOSS cusp tool). The tool normally just allows to process all sequences together (concatenated).
emboss loops galaxy workflow • 1.0k views
ADD COMMENT • link •
modified 4.5 years ago by Bjoern Gruening ♦ 5.1k • written 4.5 years ago by Daniel Elleder • 30
2
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

loops are currently not possible, but the Galaxy Team is actively working on that. Dataset collections, currently scheduled for the next Galaxy release in one month, will address your use case I think.

In the meantime try to insert the following snipped into your emboss tool.

<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1" merge_outputs="TODO"></parallelism>

Adopt the split_inputs and merge_outputs to the variables in your emboss wrapper. The snippet will automatically split your multi FASTA file into simgle FASTA files and concatenate the output of all runs into one single output. The only requirement is that the outputs can be concatenated.

 
ADD COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k
1

Dataset collections will not cover this use case, there is just a single file in this use case. Also the parallelism mechanism is really designed to address splitting for optional performance reasons - not splitting as a necessity - for this reason it is off by default and so tools depending on this would not work (by default). My recommendation would just be to write a simple Python/Perl/sh wrapper script to consume the file and repeatedly call the underlying tool.

ADD REPLY • link modified 4.5 years ago • written 4.5 years ago by jmchilton ♦ 1.1k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour