Name: muscope-18SV4
Owner: Hurwitz Lab
Description: A CyVerse app implementing "Microbial eukaryotic 18S tag-sequence processing/QC - V4 region" from protocols.io.
Created: 2017-03-04 15:00:31.0
Updated: 2017-03-21 15:00:25.0
Pushed: 2017-08-25 01:25:00.0
Homepage: null
Size: 444
Language: Python
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A CyVerse application implementing “Microbial eukaryotic 18S tag-sequence processing/QC - V4 region” as described by https://www.protocols.io/view/microbial-eukaryotic-18s-tag-sequence-processing-q-g33byqn.
This pipeline can be used in three ways:
In all cases the following command line arguments must be specified:
File path to a FASTQ file of forward reads. The corresponding file of reverse reads should also be in the same directory.
-w WORK_DP Directory path for all output. The work directory will be created if it does not exist.
-c CORE_COUNT Number of cores to use. Specify at least 1.
-p PREFIX_REGEX Regular expression that will match the forward and reverse read file prefix. For example the regular expression
^(?P
[a-zA-Z0-9]+)L001_R[12] will identify
Test001as the prefix in the file nameTest001_L001_R1_001.fastq. Use a regular expression tool such as Pythex to verify your regular expression will work with your files.–forward-primer Forward primer to be removed.
–reverse-primer Reverse primer to be removed.
–min-overlap Minimum overlap for joining paired end reads.
Installing and running this pipeline as a simple application requires
Installing QIIME is not a trivial exercise. The recommended method (see here) is to use Miniconda. Once Miniconda is installed follow these steps:
nda create -n mu python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda -c fastq-join=1.3.1
uce activate mu
$ pip install git+https://github.com/hurwitzlab/muscope-18SV4.git
The last line installs the application in the virtual environment.
Once the Python application has been installed it can be run from the command line like this:
$ pipeline
e: pipeline [-h] -f FORWARD_READS_FP -w WORK_DP -c CORE_COUNT -p
PREFIX_REGEX [--forward-primer FORWARD_PRIMER]
[--reverse-primer REVERSE_PRIMER] [--min-overlap MIN_OVERLAP]
Building the Singularity container requires sudo permissions on a Linux system, Singularity 2.3 or later, and make.
Simply using the Singularity container requires no special permissions but does require Singularity 2.3 or later.
t clone https://github.com/hurwitzlab/muscope-18SV4.git
muscope-18SV4
ke container
The container will be built in the muscope18SV4/singularity directory.
The pipeline program can be executed from the Singularity container like this:
ngularity exec singularity/muscope-18SV4.img pipeline
The command line arguments are the same as for the stand-alone Python program.
Using the CyVerse app requires a CyVerse account and membership in the muSCOPE group.