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commit 500cacfb8579ee5afc89a423ba1b6dd4dfafde66 Author: Sascha Steinbiss <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
