Ipyrad-Teaching
Category
Bioinformatics
Program On
Teaching
Version
0.7.24
Author / Distributor
Description
"ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies." More details are at ipyrad
Running Program
The last version of this application is at /usr/local/apps/eb/ipyrad/0.7.24-foss-2016b-Python-2.7.14
To use this version, please load the module with
ml ipyrad/0.7.24-foss-2016b-Python-2.7.14
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_ipyrad
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=ipyrad.%j.out
#SBATCH --error=ipyrad.%j.err
cd $SLURM_SUBMIT_DIR
ml ipyrad/0.7.24-foss-2016b-Python-2.7.14
ipyrad [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml ipyrad/0.7.24-foss-2016b-Python-2.7.14
ipyrad -h
usage: ipyrad [-h] [-v] [-r] [-f] [-q] [-d] [-n new] [-p params]
[-b [branch [branch ...]]] [-m [merge [merge ...]]] [-s steps]
[-c cores] [-t threading] [--MPI] [--preview]
[--ipcluster [ipcluster]] [--download [download [download ...]]]
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-r, --results show results summary for Assembly in params.txt and
exit
-f, --force force overwrite of existing data
-q, --quiet do not print to stderror or stdout.
-d, --debug print lots more info to ipyrad_log.txt.
-n new create new file 'params-{new}.txt' in current
directory
-p params path to params file for Assembly:
params-{assembly_name}.txt
-b [branch [branch ...]]
create a new branch of the Assembly as
params-{branch}.txt
-m [merge [merge ...]]
merge all assemblies provided into a new assembly
-s steps Set of assembly steps to perform, e.g., -s 123
(Default=None)
-c cores number of CPU cores to use (Default=0=All)
-t threading tune threading of binaries (Default=2)
--MPI connect to parallel CPUs across multiple nodes
--preview run ipyrad in preview mode. Subset the input file so
it'll runquickly so you can verify everything is
working
--ipcluster [ipcluster]
connect to ipcluster profile (default: 'default')
--download [download [download ...]]
download fastq files by accession (e.g., SRP or SRR)
* Example command-line usage:
ipyrad -n data ## create new file called params-data.txt
ipyrad -p params-data.txt ## run ipyrad with settings in params file
ipyrad -p params-data.txt -s 123 ## run only steps 1-3 of assembly.
ipyrad -p params-data.txt -s 3 -f ## run step 3, overwrite existing data.
* HPC parallelization across 32 cores
ipyrad -p params-data.txt -s 3 -c 32 --MPI
* Print results summary
ipyrad -p params-data.txt -r
* Branch/Merging Assemblies
ipyrad -p params-data.txt -b newdata
ipyrad -m newdata params-1.txt params-2.txt [params-3.txt, ...]
* Subsample taxa during branching
ipyrad -p params-data.txt -b newdata taxaKeepList.txt
* Download sequence data from SRA into directory 'sra-fastqs/'
ipyrad --download SRP021469 sra-fastqs/
* Documentation: http://ipyrad.readthedocs.io
Installation
Source code is obtained from ipyrad
System
64-bit Linux