[med-svn] [snap-aligner] 01/01: Paper metadata; update program name in docs; add zlib builddep
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Sep 30 03:06:09 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository snap-aligner.
commit ddfe2cf642aee873125b88ad2b60aab018e6a129
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
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
+
--
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