[med-svn] r16620 - trunk/packages/smalt/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-04-08 18:57:00 +0000 (Tue, 08 Apr 2014)
New Revision: 16620

Added:
   trunk/packages/smalt/trunk/debian/install
   trunk/packages/smalt/trunk/debian/smalt.1
Removed:
   trunk/packages/smalt/trunk/debian/mans/
Modified:
   trunk/packages/smalt/trunk/debian/control
   trunk/packages/smalt/trunk/debian/createmanpages
   trunk/packages/smalt/trunk/debian/manpages
   trunk/packages/smalt/trunk/debian/rules
Log:
Change installation after upstream confirmed that only smalt binary is relevant; Add Build-Depends for tests which is not yet sufficient (works with plain debuild)


Modified: trunk/packages/smalt/trunk/debian/control
===================================================================
--- trunk/packages/smalt/trunk/debian/control	2014-04-08 16:05:04 UTC (rev 16619)
+++ trunk/packages/smalt/trunk/debian/control	2014-04-08 18:57:00 UTC (rev 16620)
@@ -3,7 +3,9 @@
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+               python-biopython,
+               samtools
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/smalt/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/smalt/trunk/

Modified: trunk/packages/smalt/trunk/debian/createmanpages
===================================================================
--- trunk/packages/smalt/trunk/debian/createmanpages	2014-04-08 16:05:04 UTC (rev 16619)
+++ trunk/packages/smalt/trunk/debian/createmanpages	2014-04-08 18:57:00 UTC (rev 16620)
@@ -1,5 +1,5 @@
 #!/bin/sh
-MANDIR=debian/mans
+MANDIR=debian
 mkdir -p $MANDIR
 
 VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
@@ -7,6 +7,3 @@
 help2man --no-info --no-discard-stderr --help-option=" " \
          --name='<optional description of the program>' \
             --version-string="$VERSION" smalt > $MANDIR/smalt.1
-#help2man --no-info --no-discard-stderr --help-option=" " \
-#         --name='<optional description of the program>' \
-#            --version-string="$VERSION" basqcol > $MANDIR/basqcol.1

Added: trunk/packages/smalt/trunk/debian/install
===================================================================
--- trunk/packages/smalt/trunk/debian/install	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/install	2014-04-08 18:57:00 UTC (rev 16620)
@@ -0,0 +1 @@
+src/smalt

Modified: trunk/packages/smalt/trunk/debian/manpages
===================================================================
--- trunk/packages/smalt/trunk/debian/manpages	2014-04-08 16:05:04 UTC (rev 16619)
+++ trunk/packages/smalt/trunk/debian/manpages	2014-04-08 18:57:00 UTC (rev 16620)
@@ -1 +1 @@
-debian/mans/*.1
+debian/*.1

Modified: trunk/packages/smalt/trunk/debian/rules
===================================================================
--- trunk/packages/smalt/trunk/debian/rules	2014-04-08 16:05:04 UTC (rev 16619)
+++ trunk/packages/smalt/trunk/debian/rules	2014-04-08 18:57:00 UTC (rev 16620)
@@ -19,5 +19,12 @@
 %:
 	dh $@
 
+override_dh_auto_install:
+	# upstream install does install more files than needed
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -fr test/*.pyc test/tmp
+
 #get-orig-source:
 #	. debian/get-orig-source

Added: trunk/packages/smalt/trunk/debian/smalt.1
===================================================================
--- trunk/packages/smalt/trunk/debian/smalt.1	                        (rev 0)
+++ trunk/packages/smalt/trunk/debian/smalt.1	2014-04-08 18:57:00 UTC (rev 16620)
@@ -0,0 +1,49 @@
+.TH SMALT "1" "April 2014" "smalt 0.7.6" "User Commands"
+.SH NAME
+smalt \- Sequence Mapping and Alignment Tool
+.SH DESCRIPTION
+.PP
+SMALT efficiently aligns DNA sequencing reads with a reference genome.
+It Reads from a wide range of sequencing platforms, for example Illumina,
+Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
+paired reads.
+.PP
+The software employs a perfect hash index of short words (< 20
+nucleotides long), sampled at equidistant steps along the genomic
+reference sequences.
+.PP
+For each read, potentially matching segments in the reference are
+identified from seed matches in the index and subsequently aligned with
+the read using a banded Smith-Waterman algorithm.
+.PP
+The best gapped alignments of each read is reported including a score
+for the reliability of the best mapping. The user can adjust the
+trade-off between sensitivity and speed by tuning the length and spacing
+of the hashed words.
+.PP
+A mode for the detection of split (chimeric) reads is provided.
+Multi-threaded program execution is supported.
+.SH SYNOPSIS
+.B smalt
+\fB<task>\fR \fI[TASK_OPTIONS] [<index_name> <file_name_A> [<file_name_B>]]\fR
+.SS "Available tasks:"
+.TP
+smalt check
+\- checks FASTA/FASTQ input
+.TP
+smalt help
+\- prints a brief summary of this software
+.TP
+smalt index
+\- builds an index of k\-mer words for the reference
+.TP
+smalt map
+\- maps single or paired reads onto the reference
+.TP
+smalt sample
+\- sample insert sizes for paired reads
+.IP
+smalt version \- prints version information
+.SS "Help on individual tasks:"
+.IP
+smalt <task> \fB\-H\fR