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commit ddfe2cf642aee873125b88ad2b60aab018e6a129 Author: Michael R. Crusoe <[email protected]> Date: Sun Sep 27 17:59:13 2015 -0700 Paper metadata; update program name in docs; add zlib builddep --- debian/control | 3 +- debian/patches/finish-rename | 85 ++++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 18 ++-------- debian/upstream/metadata | 20 +++++------ 5 files changed, 99 insertions(+), 28 deletions(-) diff --git a/debian/control b/debian/control index e6eb30b..fe9c9b5 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,8 @@ Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Michael R. Crusoe <[email protected]> Build-Depends: debhelper (>= 9), - help2man + help2man, + zlib1g-dev Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/ diff --git a/debian/patches/finish-rename b/debian/patches/finish-rename new file mode 100644 index 0000000..457f13d --- /dev/null +++ b/debian/patches/finish-rename @@ -0,0 +1,85 @@ +Author: Michael R. Crusoe +Description: Change the name of program in docs +--- snap-aligner.orig/SNAPLib/AlignerContext.cpp ++++ snap-aligner/SNAPLib/AlignerContext.cpp +@@ -396,9 +396,9 @@ + AlignerOptions *options; + + if (paired) { +- options = new PairedAlignerOptions("snap paired <index-dir> <inputFile(s)> [<options>] where <input file(s)> is a list of files to process.\n"); ++ options = new PairedAlignerOptions("snap-aligner paired <index-dir> <inputFile(s)> [<options>] where <input file(s)> is a list of files to process.\n"); + } else { +- options = new AlignerOptions("snap single <index-dir> <inputFile(s)> [<options>] where <input file(s)> is a list of files to process.\n"); ++ options = new AlignerOptions("snap-aligner single <index-dir> <inputFile(s)> [<options>] where <input file(s)> is a list of files to process.\n"); + } + + options->extra = extension->extraOptions(); +--- snap-aligner.orig/SNAPLib/AlignerOptions.cpp ++++ snap-aligner/SNAPLib/AlignerOptions.cpp +@@ -200,7 +200,7 @@ + "alignment, followed by a comma (separated by a space from the other parameters) followed by the\n" + "parameters for the next alignment (including single or paired). You may have as many of these\n" + "as you please. If two consecutive alignments use the same index, it will not be reloaded.\n" +- "So, for example, you could do 'snap single hg19-20 foo.fq -o foo.sam , paired hg19-20 end1.fq end2.fq -o paired.sam'\n" ++ "So, for example, you could do 'snap-aligner single hg19-20 foo.fq -o foo.sam , paired hg19-20 end1.fq end2.fq -o paired.sam'\n" + "and it would not reload the index between the single and paired alignments.\n", + "SNAP doesn't parse the options for later runs until the earlier ones have completed, so if you make\n" + "an error in one, it may take a while for you to notice. So, be careful (or check back shortly after\n" +@@ -225,7 +225,7 @@ + "explicitly specify the type. But really, that's just confusing and you shouldn't do it.\n" + "Input and output may also be from/to stdin/stdout. To do that, use a - for the input or output file\n" + "name and give an explicit type specifier. So, for example, \n" +- "snap single myIndex -fastq - -o -sam -\n" ++ "snap-aligner aligner single myIndex -fastq - -o -sam -\n" + "would read FASTQ from stdin and write SAM to stdout.\n" + ); + } +@@ -957,7 +957,7 @@ + } + } else { + if (snapFile->isStdio) { +- WriteErrorMessage("Stdio IO always requires an explicit file type. So, for example, do 'snap single index-directory -fastq -' to read FASTQ from stdin\n"); ++ WriteErrorMessage("Stdio IO always requires an explicit file type. So, for example, do 'snap-aligner single index-directory -fastq -' to read FASTQ from stdin\n"); + } else { + WriteErrorMessage("Unknown file type for file name '%s', please specify file type with -fastq, -sam, -bam, etc.\n", snapFile->fileName); + } +--- snap-aligner.orig/SNAPLib/CommandProcessor.cpp ++++ snap-aligner/SNAPLib/CommandProcessor.cpp +@@ -40,7 +40,7 @@ + static void usage() + { + WriteErrorMessage( +- "Usage: snap <command> [<options>]\n" ++ "Usage: snap-alinger <command> [<options>]\n" + "Commands:\n" + " index build a genome index\n" + " single align single-end reads\n" +@@ -57,7 +57,7 @@ + // + // The error cases in index build don't really free memory properly, so we just don't allows it in daemon mode. + // +- WriteErrorMessage("The index command is not available in daemon mode. Please run 'snap index' directly.\n"); ++ WriteErrorMessage("The index command is not available in daemon mode. Please run 'snap-aligner index' directly.\n"); + } + } else if (strcmp(argv[1], "single") == 0 || strcmp(argv[1], "paired") == 0) { + for (int i = 1; i < argc; /* i is increased below */) { +@@ -84,7 +84,7 @@ + + static void daemonUsage() + { +- fprintf(stderr, "Usage: snap daemon [Named pipe name]\n"); ++ fprintf(stderr, "Usage: snap-aligner daemon [Named pipe name]\n"); + soft_exit_no_print(1); // Don't use soft_exit, it's confusing people to get an "error" message after the usage + } + +--- snap-aligner.orig/SNAPLib/GenomeIndex.cpp ++++ snap-aligner/SNAPLib/GenomeIndex.cpp +@@ -51,7 +51,7 @@ + static void usage() + { + WriteErrorMessage( +- "Usage: snap index <input.fa> <output-dir> [<options>]\n" ++ "Usage: snap-aligner index <input.fa> <output-dir> [<options>]\n" + "Options:\n" + " -s Seed size (default: %d)\n" + " -h Hash table slack (default: %.1f)\n" diff --git a/debian/patches/series b/debian/patches/series index e057d52..5acb609 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ spelling +finish-rename diff --git a/debian/rules b/debian/rules index a49d252..5511f2a 100755 --- a/debian/rules +++ b/debian/rules @@ -1,20 +1,7 @@ #!/usr/bin/make -f -# DH_VERBOSE := 1 - -# some helpful variables - uncomment them if needed -# shamelessly stolen from http://jmtd.net/log/awk/ DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') -#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') -#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') -#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) -#GIT_TAG := $(subst ~,_,$(VERSION)) - -# alternatively to manually set those variables, you can -# include /usr/share/dpkg/default.mk -# and use what is set there. - %: dh $@ @@ -26,7 +13,7 @@ override_dh_auto_build: dh_auto_build help2man --no-discard-stderr --no-info --version-string="${VERSION}" \ --name "scalable nucleotide alignment program" \ - --help-option=" " snap-aligner > debian/snap-aligner.1 + --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="${VERSION}" \ --include=debian/snap-aligner-$${option}-man-include \ @@ -34,5 +21,4 @@ override_dh_auto_build: debian/snap-aligner-$${option}.1; done help2man --no-discard-stderr --no-info --version-string="${VERSION}" \ --name "scalable nucleotide alignment program" \ - --help-option=" " SNAPCommand > debian/SNAPCommand.1 - + --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 diff --git a/debian/upstream/metadata b/debian/upstream/metadata index d8b5812..31dff5d 100644 --- a/debian/upstream/metadata +++ b/debian/upstream/metadata @@ -1,12 +1,10 @@ Reference: - Author: - Title: - Journal: - Year: - Volume: - Number: - Pages: - DOI: - PMID: - URL: - eprint: + Author: Matei Zaharia and William J. Bolosky and Kristal Curtis and Armando + Fox and David Patterson and Scott Shenker and Ion Stoica and Richard + M. Karp and Taylor Sittler + Title: Faster and More Accurate Sequence Alignment with SNAP + Journal: arXiv preprint arXiv:1111.5572 + Year: 2011 + URL: http://arxiv.org/pdf/1111.5572v1 + eprint: arXiv:1111.5572 + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snap-aligner.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
