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 <[email protected]> Uploaders: Andreas Tille <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
