[med-svn] [spades] 04/06: add rnaSPAdes
Sascha Steinbiss
satta at debian.org
Sun Jul 24 13:35:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository spades.
commit 500cacfb8579ee5afc89a423ba1b6dd4dfafde66
Author: Sascha Steinbiss <satta at debian.org>
Date: Sun Jul 24 12:07:30 2016 +0000
add rnaSPAdes
---
debian/links | 2 +
debian/man_src/{spades.1.adoc => rnaspades.1.adoc} | 52 ++--------------------
debian/man_src/spades.1.adoc | 5 ++-
debian/rules | 1 +
debian/tests/run-upstreams-tests | 1 +
5 files changed, 12 insertions(+), 49 deletions(-)
diff --git a/debian/links b/debian/links
index 78ab128..81d0f27 100644
--- a/debian/links
+++ b/debian/links
@@ -8,6 +8,8 @@ usr/bin/spades usr/bin/metaspades.py
usr/bin/spades usr/bin/metaspades
usr/bin/spades usr/bin/plasmidspades.py
usr/bin/spades usr/bin/plasmidspades
+usr/bin/spades usr/bin/rnaspades.py
+usr/bin/spades usr/bin/rnaspades
usr/bin/bwa usr/lib/spades/bin/bwa-spades
usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz
diff --git a/debian/man_src/spades.1.adoc b/debian/man_src/rnaspades.1.adoc
similarity index 55%
copy from debian/man_src/spades.1.adoc
copy to debian/man_src/rnaspades.1.adoc
index e2f6506..93096fe 100644
--- a/debian/man_src/spades.1.adoc
+++ b/debian/man_src/rnaspades.1.adoc
@@ -1,18 +1,16 @@
-= spades(1)
+= rnaspades(1)
## NAME
-spades - SPAdes genome assembler
+rnaspades - SPAdes genome assembler (rnaSPAdes mode)
## SYNOPSIS
-*spades* [options] -o <output_dir>
+*rnaspades* [options] -o <output_dir>
## DESCRIPTION
-*spades* is the main executable for the **SPAdes** software. It
-assembles genomic reads given to it and places the resulting assembly in
-<output_dir>.
+*rnaspades* runs **SPAdes** in rnaSPAdes mode.
## OPTIONS
@@ -21,15 +19,6 @@ assembles genomic reads given to it and places the resulting assembly in
*-o* <output_dir>::
directory to store all the resulting files (required)
-*--sc*::
- this flag is required for MDA (single-cell) data
-
-*--meta*::
- this flag is required for metagenomic sample data
-
-*--plasmid*::
- Runs plasmidSPAdes pipeline for plasmid detection
-
*--iontorrent*::
this flag is required for IonTorrent data
@@ -66,36 +55,6 @@ assembles genomic reads given to it and places the resulting assembly in
orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
*--s<#>* <filename>::
file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-12* <filename>::
- file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-1* <filename>::
- file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-2* <filename>::
- file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-s* <filename>::
- file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-<or>*::
- orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-*--hqmp<#>-12* <filename>::
- file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-1* <filename>::
- file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-2* <filename>::
- file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-s* <filename>::
- file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-<or>*::
- orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-*--nxmate<#>-1* <filename>::
- file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
-*--nxmate<#>-2* <filename>::
- file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
-*--sanger* <filename>::
- file with Sanger reads
-*--pacbio* <filename>::
- file with PacBio reads
-*--nanopore* <filename>::
- file with Nanopore reads
*--trusted-contigs* <filename>::
file with trusted contigs
*--untrusted-contigs* <filename>::
@@ -107,8 +66,6 @@ assembles genomic reads given to it and places the resulting assembly in
runs only read error correction (without assembling)
*--only-assembler*::
runs only assembling (without read error correction)
-*--careful*::
- tries to reduce number of mismatches and short indels
*--continue*::
continue run from the last available check-point
*--restart-from* <cp>::
@@ -134,4 +91,3 @@ assembles genomic reads given to it and places the resulting assembly in
coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
*--phred-offset* <33 or 64>::
PHRED quality offset in the input reads (33 or 64) [default: auto-detect]
-
diff --git a/debian/man_src/spades.1.adoc b/debian/man_src/spades.1.adoc
index e2f6506..35768eb 100644
--- a/debian/man_src/spades.1.adoc
+++ b/debian/man_src/spades.1.adoc
@@ -27,8 +27,11 @@ assembles genomic reads given to it and places the resulting assembly in
*--meta*::
this flag is required for metagenomic sample data
+*--rna*::
+ this flag is required for RNA-seq data
+
*--plasmid*::
- Runs plasmidSPAdes pipeline for plasmid detection
+ runs plasmidSPAdes pipeline for plasmid detection
*--iontorrent*::
this flag is required for IonTorrent data
diff --git a/debian/rules b/debian/rules
index 756b4b7..1da7205 100755
--- a/debian/rules
+++ b/debian/rules
@@ -55,6 +55,7 @@ override_dh_auto_test:
$(TMPDIR)/bin/spades.py --test
$(TMPDIR)/bin/dipspades.py --test
$(TMPDIR)/bin/metaspades.py --test
+ $(TMPDIR)/bin/rnaspades.py --test
# Difficult to test truSPAdes before installing because bwa-spades
# is still not in the right place. Let's do this later in an
# autopkgtest.
diff --git a/debian/tests/run-upstreams-tests b/debian/tests/run-upstreams-tests
index aed9d5c..7d19a79 100755
--- a/debian/tests/run-upstreams-tests
+++ b/debian/tests/run-upstreams-tests
@@ -11,3 +11,4 @@ dipspades --test
spades --test
truspades --test
metaspades --test
+rnaspades --test
--
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