Commits

Commits on Jan 12, 2021

adds deprecation note
nellore
committedJan 12, 2021

Commits on Jul 9, 2020

adds unit test to alignment_handlers
nellore
committedJul 9, 2020

Commits on Apr 9, 2019

embed parsed_md
BenLangmead
committedApr 9, 2019

Commits on Apr 8, 2019

make more portable
BenLangmead
committedApr 8, 2019
some attempts to make this script more portable
BenLangmead
committedApr 8, 2019

Commits on Mar 15, 2018

switched to use sratoolkit 2.8.0-2 due to fastq-dump --stdout timing out
ChristopherWilks
committedMar 15, 2018

Commits on Mar 4, 2018

patches bowtie2-build in travis setup for pypy
nellore
committedMar 4, 2018
uses bowtie2 2.3.4.1
nellore
committedMar 4, 2018
specifies samtools version to install in travis.yml
nellore
committedMar 4, 2018
Merge branch 'master' of https://github.com/nellore/rail
nellore
committedMar 4, 2018
updates dependencies
nellore
committedMar 4, 2018
Merge pull request #86 from BenLangmead/fix_lifecycle_quote
nellore
committedMar 4, 2018

Commits on Feb 4, 2018

enables --keep-alive for coverage.py in elastic mode
nellore
committedFeb 4, 2018

Commits on Jan 10, 2018

quote rules
BenLangmead
committedJan 10, 2018

Commits on Dec 29, 2017

Commits on Dec 28, 2017

Merge branch 'master' of https://github.com/nellore/rail
nellore
committedDec 28, 2017
fixes issue wipassing temp dir to sort in rail
nellore
committedDec 28, 2017
fixes issue wipassing temp dir to sort in rail
nellore
committedDec 28, 2017

Commits on Dec 23, 2017

fixes misplaced joins in exception code in ansibles.py
nellore
committedDec 23, 2017
fixes command list in ansibles
nellore
committedDec 23, 2017
avoids use of os.devnull in python subprocesses
nellore
committedDec 23, 2017

Commits on Dec 22, 2017

adds comma
nellore
committedDec 22, 2017
attempts no null_stream
nellore
committedDec 22, 2017
prints devnull
nellore
committedDec 22, 2017
tries different command
nellore
committedDec 22, 2017
writes different command
nellore
committedDec 22, 2017
writes exit code to log
nellore
committedDec 22, 2017
tries invoking bowtie2-build alone in realign_reads
nellore
committedDec 22, 2017
checks bowtie2-build executable
nellore
committedDec 22, 2017
executes with shell=True
nellore
committedDec 22, 2017
raises runtimeerror
nellore
committedDec 22, 2017
prints fasta size
nellore
committedDec 22, 2017
does not raise runtimeerror in realign_reads
nellore
committedDec 22, 2017
does not print tmpdir path
nellore
committedDec 22, 2017