Author: tille Date: 2015-01-20 11:05:45 +0000 (Tue, 20 Jan 2015) New Revision: 18596
Removed: trunk/packages/vsearch/trunk/debian/createmanpages trunk/packages/vsearch/trunk/debian/vsearch.1 Modified: trunk/packages/vsearch/trunk/debian/README.source trunk/packages/vsearch/trunk/debian/copyright trunk/packages/vsearch/trunk/debian/rules trunk/packages/vsearch/trunk/debian/tests/run-unit-test trunk/packages/vsearch/trunk/debian/vsearch-data.install trunk/packages/vsearch/trunk/debian/vsearch.docs trunk/packages/vsearch/trunk/debian/vsearch.manpages Log: Remove uncompressed copies of large data files from source tarball and data package and rather recreate these files if testsuite will be run; use upstream manpage Modified: trunk/packages/vsearch/trunk/debian/README.source =================================================================== --- trunk/packages/vsearch/trunk/debian/README.source 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/README.source 2015-01-20 11:05:45 UTC (rev 18596) @@ -3,4 +3,16 @@ I'm sure they'll sort this at some point, but for now we have to compile the whole thing three times. -Tim Booth + -- Tim Booth <[email protected]> Fri, 09 Jan 2015 17:13:35 +0000 + + +The file data/BioMarKs.fsa.gz has the very same content as +data/BioMarKs.fsa.bz2 but just a different compression method. +To save disk space the former is deleted from source tarball and +recreated in the test target where it is needed. + +The same is true for data/PR2-18S-rRNA-V4.fsa which is just an +uncompressed copy of data/PR2-18S-rRNA-V4.fsa.bz2 + + -- Andreas Tille <[email protected]> Wed, 14 Jan 2015 10:40:22 +0000 + Modified: trunk/packages/vsearch/trunk/debian/copyright =================================================================== --- trunk/packages/vsearch/trunk/debian/copyright 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/copyright 2015-01-20 11:05:45 UTC (rev 18596) @@ -3,6 +3,14 @@ Upstream-Contact: Torbjørn Rognes Source: https://github.com/torognes/vsearch/ Files-Excluded: bin/* + data/BioMarKs.fsa.gz + data/PR2-18S-rRNA-V4.fsa +Comment: data/BioMarKs.fsa.gz has the very same content as + data/BioMarKs.fsa.bz2 but just a different compression method. + To save disk space the former is deleted from source tarball and + recreated in the test target where it is needed. + The same is true for data/PR2-18S-rRNA-V4.fsa which is just + an uncompressed copy of data/PR2-18S-rRNA-V4.fsa.bz2 Files: * Copyright: © 2014-2015 Torbjorn Rognes & Tomas Flouri Deleted: trunk/packages/vsearch/trunk/debian/createmanpages =================================================================== --- trunk/packages/vsearch/trunk/debian/createmanpages 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/createmanpages 2015-01-20 11:05:45 UTC (rev 18596) @@ -1,16 +0,0 @@ -#!/bin/sh -MANDIR=debian -mkdir -p $MANDIR - -VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` - -help2man --no-info --no-discard-stderr \ - --name='tool for processing metagenomic sequences' \ - --version-string="$VERSION" vsearch > $MANDIR/vsearch.1 - -cat <<EOT -Please enhance the help2man output. -The following web page might be helpful in doing so: - http://liw.fi/manpages/ -EOT - Modified: trunk/packages/vsearch/trunk/debian/rules =================================================================== --- trunk/packages/vsearch/trunk/debian/rules 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/rules 2015-01-20 11:05:45 UTC (rev 18596) @@ -4,6 +4,7 @@ #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') +testdir := $(CURDIR)/debian/$(pkg)-data/usr/share/doc/$(pkg)/tests %: dh $@ --sourcedirectory=src @@ -16,30 +17,39 @@ dh_auto_clean dh_auto_build markdown_py -f README.html README.md + markdown_py -f data/README.html data/README.md override_dh_auto_clean: dh_auto_clean rm -f src/vsearch-gz src/vsearch-bz override_dh_auto_test: + # restore data files from original tarball as well as those files needed for the full testsuite + cd data && bunzip2 --keep BioMarKs.fsa.bz2 && gzip --keep --rsyncable BioMarKs.fsa + cd data && bunzip2 --keep PR2-18S-rRNA-V4.fsa.bz2 && gzip --keep --rsyncable PR2-18S-rRNA-V4.fsa cd data && tar -xvzf simm.tar.gz cd test && \ for t in *.sh ; do \ bash $$t v ; \ done + rm -f data/BioMarKs.fsa data/BioMarKs.fsa.gz \ + data/PR2-18S-rRNA-V4.fsa data/PR2-18S-rRNA-V4.fsa.gz override_dh_clean: dh_clean rm -rf data/simm find test -mindepth 1 -not -name '*.sh' -delete - rm -f README.html + rm -f README.html data/README.html rm -f *.out override_dh_install: dh_install # tweak path tp vsearch binary in test scripts - mkdir -p $(CURDIR)/debian/$(pkg)-data/usr/share/doc/$(pkg)/test - for tst in test/*.sh ; do sed 's?\.\./src/vsearch?/usr/bin/vsearch?' $${tst} > $(CURDIR)/debian/$(pkg)-data/usr/share/doc/$(pkg)/$${tst} ; done + mkdir -p $(testdir)/eval + for tst in eval/*.sh ; do sed 's?\.\./src/vsearch?/usr/bin/vsearch?' $${tst} > $(testdir)/$${tst} ; done + sed -i 's?#\(VSEARCH=/usr/bin/vsearch\)?\1?' $(testdir)/eval/eval.sh ; done + mkdir -p $(testdir)/test + for tst in test/*.sh ; do sed 's?\.\./src/vsearch?/usr/bin/vsearch?' $${tst} > $(testdir)/$${tst} ; done get-orig-source: uscan --verbose --force-download --repack --compression xz Modified: trunk/packages/vsearch/trunk/debian/tests/run-unit-test =================================================================== --- trunk/packages/vsearch/trunk/debian/tests/run-unit-test 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/tests/run-unit-test 2015-01-20 11:05:45 UTC (rev 18596) @@ -2,18 +2,20 @@ pkg=vsearch if [ "$ADTTMP" = "" ] ; then - ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` + ADTTMP=`mktemp -d /var/tmp/${pkg}-test.XXXXXX` fi cd $ADTTMP mkdir -p data cd data tar xaf /usr/share/doc/${pkg}/examples/simm.tar.gz cp -a /usr/share/doc/${pkg}/examples/[A-Z]* . -gunzip BioMarKs50k* [PR]*.gz cd .. -cp -a /usr/share/doc/${pkg}/test . -cd test +cp -a /usr/share/doc/${pkg}/tests/eval . +cp -a /usr/share/doc/${pkg}/tests/test . find . -type f -name "*.gz" -exec gunzip \{\} \; +cd data && bunzip2 --keep BioMarKs.fsa.bz2 && gzip --keep --rsyncable BioMarKs.fsa && \ + bunzip2 --keep PR2-18S-rRNA-V4.fsa.bz2 && gzip --keep --rsyncable PR2-18S-rRNA-V4.fsa +cd ../test for t in *.sh ; do \ bash $t v ; \ done Modified: trunk/packages/vsearch/trunk/debian/vsearch-data.install =================================================================== --- trunk/packages/vsearch/trunk/debian/vsearch-data.install 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/vsearch-data.install 2015-01-20 11:05:45 UTC (rev 18596) @@ -4,3 +4,6 @@ data/PR2-18S-rRNA-V4.fsa* usr/share/doc/vsearch/examples data/Rfam_11_0.* usr/share/doc/vsearch/examples data/Rfam_9_1.fasta usr/share/doc/vsearch/examples +data/README.html usr/share/doc/vsearch/examples +eval/*.pl usr/share/doc/vsearch/tests/eval +eval/*.txt usr/share/doc/vsearch/tests/eval Deleted: trunk/packages/vsearch/trunk/debian/vsearch.1 =================================================================== --- trunk/packages/vsearch/trunk/debian/vsearch.1 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/vsearch.1 2015-01-20 11:05:45 UTC (rev 18596) @@ -1,396 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2. -.TH VSEARCH "1" "January 2015" "vsearch 1.0.7" "User Commands" -.SH NAME -vsearch \- tool for processing metagenomic sequences -.SH SYNOPSIS -.B vsearch -[\fI\,OPTIONS\/\fR] -.SH DESCRIPTION -.PP -64-bit multithreaded tool for processing metagenomic sequences, including -searching, clustering, chimera detection, dereplication, sorting, masking -and shuffling -.PP -The aim of this project is to create an alternative to the USEARCH tool -developed by Robert C. Edgar (2010). -.SH OPTIONS -.TP -\fB\-\-help\fR -display help information -.TP -\fB\-\-version\fR -display version information -.TP -\fB\-\-fasta_width\fR INT -width of FASTA seq lines, 0 for no wrap (80) -.TP -\fB\-\-maxseqlength\fR INT -maximum sequence length (50000) -.TP -\fB\-\-minseqlength\fR INT -min seq length (clust/derep/search: 32, other:1) -.TP -\fB\-\-notrunclabels\fR -do not truncate labels at first space -.TP -\fB\-\-threads\fR INT -number of threads to use, zero for all cores (0) -.PP -Alignment options (most searching options also apply) -.TP -\fB\-\-allpairs_global\fR FILENAME -perform global alignment of all sequence pairs -.TP -\fB\-\-alnout\fR FILENAME -filename for human\-readable alignment output -.TP -\fB\-\-acceptall\fR -output all pairwise alignments -.PP -Chimera detection options -.TP -\fB\-\-abskew\fR REAL -min abundance ratio of parent vs chimera (2.0) -.TP -\fB\-\-alignwidth\fR INT -width of alignment in uchimealn output (80) -.TP -\fB\-\-chimeras\fR FILENAME -output chimeric sequences to file -.TP -\fB\-\-db\fR FILENAME -reference database for \fB\-\-uchime_ref\fR -.TP -\fB\-\-dn\fR REAL -\&'no' vote pseudo\-count (1.4) -.TP -\fB\-\-mindiffs\fR INT -minimum number of differences in segment (3) -.TP -\fB\-\-mindiv\fR REAL -minimum divergence from closest parent (0.8) -.TP -\fB\-\-minh\fR REAL -minimum score (0.28) -.TP -\fB\-\-nonchimeras\fR FILENAME -output non\-chimeric sequences to file -.TP -\fB\-\-self\fR -exclude identical labels for \fB\-\-uchime_ref\fR -.TP -\fB\-\-selfid\fR -exclude identical sequences for \fB\-\-uchime_ref\fR -.TP -\fB\-\-uchime_denovo\fR FILENAME -detect chimeras de novo -.TP -\fB\-\-uchime_ref\fR FILENAME -detect chimeras using a reference database -.TP -\fB\-\-uchimealns\fR FILENAME -output chimera alignments to file -.TP -\fB\-\-uchimeout\fR FILENAME -output to chimera info to tab\-separated file -.TP -\fB\-\-uchimeout5\fR -make output compatible with uchime version 5 -.TP -\fB\-\-xn\fR REAL -\&'no' vote weight (8.0) -.PP -Clustering options (most searching options also apply) -.TP -\fB\-\-centroids\fR FILENAME -output centroid sequences to FASTA file -.TP -\fB\-\-cluster_fast\fR FILENAME -cluster sequences fast -.HP -\fB\-\-cluster_smallmem\fR FILENAME cluster sequences using a small amount of memory -.TP -\fB\-\-clusters\fR STRING -output each cluster to a separate FASTA file -.TP -\fB\-\-consout\fR FILENAME -output cluster consensus sequences to FASTA file -.TP -\fB\-\-cons_truncate\fR -do not ignore terminal gaps in MSA for consensus -.TP -\fB\-\-id\fR REAL -reject if identity lower -.TP -\fB\-\-iddef\fR INT -id definition, 0\-4=CD\-HIT,all,int,MBL,BLAST (2) -.TP -\fB\-\-msaout\fR FILENAME -output multiple seq. alignments to FASTA file -.TP -\fB\-\-qmask\fR none|dust|soft -mask seqs with dust, soft or no method (dust) -.TP -\fB\-\-sizein\fR -read abundance annotation from input -.TP -\fB\-\-sizeout\fR -write cluster abundances to centroid file -.TP -\fB\-\-strand\fR plus|both -cluster using plus or both strands (plus) -.TP -\fB\-\-uc\fR FILENAME -filename for UCLUST\-like output -.TP -\fB\-\-usersort\fR -indicate that input sequences are presorted -.PP -Dereplication options -.HP -\fB\-\-derep_fulllength\fR FILENAME dereplicate sequences in the given FASTA file -.TP -\fB\-\-maxuniquesize\fR INT -maximum abundance for output from dereplication -.TP -\fB\-\-minuniquesize\fR INT -minimum abundance for output from dereplication -.TP -\fB\-\-output\fR FILENAME -output FASTA file -.TP -\fB\-\-sizein\fR -read abundance annotation from input -.TP -\fB\-\-sizeout\fR -write abundance annotation to output -.TP -\fB\-\-strand\fR plus|both -dereplicate plus or both strands (plus) -.TP -\fB\-\-topn\fR INT -output just the n most abundant sequences -.TP -\fB\-\-uc\fR FILENAME -filename for UCLUST\-like output -.PP -Masking options -.TP -\fB\-\-hardmask\fR -mask by replacing with N instead of lower case -.TP -\fB\-\-maskfasta\fR FILENAME -mask sequences in the given FASTA file -.TP -\fB\-\-output\fR FILENAME -output to specified FASTA file -.TP -\fB\-\-qmask\fR none|dust|soft -mask seqs with dust, soft or no method (dust) -.PP -Searching options -.TP -\fB\-\-alnout\fR FILENAME -filename for human\-readable alignment output -.TP -\fB\-\-blast6out\fR FILENAME -filename for blast\-like tab\-separated output -.TP -\fB\-\-db\fR FILENAME -filename for FASTA formatted database for search -.TP -\fB\-\-dbmask\fR none|dust|soft -mask db with dust, soft or no method (dust) -.TP -\fB\-\-dbmatched\fR FILENAME -FASTA file for matching database sequences -.TP -\fB\-\-dbnotmatched\fR FILENAME -FASTA file for non\-matching database sequences -.TP -\fB\-\-fastapairs\fR FILENAME -FASTA file with pairs of query and target -.TP -\fB\-\-fulldp\fR -full dynamic programming alignment (always on) -.TP -\fB\-\-gapext\fR STRING -penalties for gap extension (2I/1E) -.TP -\fB\-\-gapopen\fR STRING -penalties for gap opening (20I/2E) -.TP -\fB\-\-hardmask\fR -mask by replacing with N instead of lower case -.TP -\fB\-\-id\fR REAL -reject if identity lower -.TP -\fB\-\-iddef\fR INT -id definition, 0\-4=CD\-HIT,all,int,MBL,BLAST (2) -.TP -\fB\-\-idprefix\fR INT -reject if first n nucleotides do not match -.TP -\fB\-\-idsuffix\fR INT -reject if last n nucleotides do not match -.TP -\fB\-\-leftjust\fR -reject if terminal gaps at alignment left end -.TP -\fB\-\-match\fR INT -score for match (2) -.TP -\fB\-\-matched\fR FILENAME -FASTA file for matching query sequences -.TP -\fB\-\-maxaccepts\fR INT -number of hits to accept and show per strand (1) -.TP -\fB\-\-maxdiffs\fR INT -reject if more substitutions or indels -.TP -\fB\-\-maxgaps\fR INT -reject if more indels -.TP -\fB\-\-maxhits\fR INT -maximum number of hits to show (unlimited) -.TP -\fB\-\-maxid\fR REAL -reject if identity higher -.TP -\fB\-\-maxqsize\fR INT -reject if query abundance larger -.TP -\fB\-\-maxqt\fR REAL -reject if query/target length ratio higher -.TP -\fB\-\-maxrejects\fR INT -number of non\-matching hits to consider (32) -.TP -\fB\-\-maxsizeratio\fR REAL -reject if query/target abundance ratio higher -.TP -\fB\-\-maxsl\fR REAL -reject if shorter/longer length ratio higher -.TP -\fB\-\-maxsubs\fR INT -reject if more substitutions -.TP -\fB\-\-mid\fR REAL -reject if percent identity lower, ignoring gaps -.TP -\fB\-\-mincols\fR INT -reject if alignment length shorter -.TP -\fB\-\-minqt\fR REAL -reject if query/target length ratio lower -.TP -\fB\-\-minsizeratio\fR REAL -reject if query/target abundance ratio lower -.TP -\fB\-\-minsl\fR REAL -reject if shorter/longer length ratio lower -.TP -\fB\-\-mintsize\fR INT -reject if target abundance lower -.TP -\fB\-\-mismatch\fR INT -score for mismatch (\fB\-4\fR) -.TP -\fB\-\-notmatched\fR FILENAME -FASTA file for non\-matching query sequences -.TP -\fB\-\-output_no_hits\fR -output non\-matching queries to output files -.TP -\fB\-\-qmask\fR none|dust|soft -mask query with dust, soft or no method (dust) -.TP -\fB\-\-query_cov\fR REAL -reject if fraction of query seq. aligned lower -.TP -\fB\-\-rightjust\fR -reject if terminal gaps at alignment right end -.TP -\fB\-\-rowlen\fR INT -width of alignment lines in alnout output (64) -.TP -\fB\-\-self\fR -reject if labels identical -.TP -\fB\-\-selfid\fR -reject if sequences identical -.TP -\fB\-\-sizeout\fR -write abundance annotation to output -.TP -\fB\-\-strand\fR plus|both -search plus or both strands (plus) -.TP -\fB\-\-target_cov\fR REAL -reject if fraction of target seq. aligned lower -.TP -\fB\-\-top_hits_only\fR -output only hits with identity equal to the best -.TP -\fB\-\-uc\fR FILENAME -filename for UCLUST\-like output -.TP -\fB\-\-uc_allhits\fR -show all, not just top hit with uc output -.TP -\fB\-\-usearch_global\fR FILENAME -filename of queries for global alignment search -.TP -\fB\-\-userfields\fR STRING -fields to output in userout file -.TP -\fB\-\-userout\fR FILENAME -filename for user\-defined tab\-separated output -.TP -\fB\-\-weak_id\fR REAL -include aligned hits with >= id; continue search -.TP -\fB\-\-wordlength\fR INT -length of words for database index 3\-15 (8) -.PP -Shuffling options -.TP -\fB\-\-output\fR FILENAME -output to specified FASTA file -.TP -\fB\-\-seed\fR INT -seed for PRNG, zero to use random data source (0) -.TP -\fB\-\-shuffle\fR FILENAME -shuffle order of sequences pseudo\-randomly -.TP -\fB\-\-topn\fR INT -output just first n sequences -.PP -Sorting options -.TP -\fB\-\-maxsize\fR INT -maximum abundance for sortbysize -.TP -\fB\-\-minsize\fR INT -minimum abundance for sortbysize -.TP -\fB\-\-output\fR FILENAME -output FASTA file -.TP -\fB\-\-relabel\fR STRING -relabel with this prefix string after sorting -.TP -\fB\-\-sizeout\fR -add abundance annotation to output -.TP -\fB\-\-sortbylength\fR FILENAME -sort sequences by length in given FASTA file -.TP -\fB\-\-sortbysize\fR FILENAME -abundance sort sequences in given FASTA file -.TP -\fB\-\-topn\fR INT -output just top n seqs after sorting Modified: trunk/packages/vsearch/trunk/debian/vsearch.docs =================================================================== --- trunk/packages/vsearch/trunk/debian/vsearch.docs 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/vsearch.docs 2015-01-20 11:05:45 UTC (rev 18596) @@ -1 +1,2 @@ *.html +doc/*.pdf Modified: trunk/packages/vsearch/trunk/debian/vsearch.manpages =================================================================== --- trunk/packages/vsearch/trunk/debian/vsearch.manpages 2015-01-19 21:36:02 UTC (rev 18595) +++ trunk/packages/vsearch/trunk/debian/vsearch.manpages 2015-01-20 11:05:45 UTC (rev 18596) @@ -1 +1 @@ -debian/*.1 +doc/*.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
