[med-svn] [sickle] 02/10: As requested by Andreas
Andreas Tille
tille at debian.org
Sun Nov 19 15:28:06 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sickle.
commit 2fb8c4b6232e55db9c0f114f1a8dca619a0352ae
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Tue Jun 23 16:40:40 2015 +0000
As requested by Andreas
---
debian/changelog | 18 ++++++++++++++++++
debian/compat | 1 +
debian/control | 33 +++++++++++++++++++++++++++++++++
debian/copyright | 27 +++++++++++++++++++++++++++
debian/docs | 1 +
debian/install | 1 +
debian/manpages | 1 +
debian/patches/makefile_ldflags | 20 ++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 21 +++++++++++++++++++++
debian/source/format | 1 +
11 files changed, 125 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..4ed6ddd
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,18 @@
+sickle (0.94-1biolinux1.1) trusty; urgency=low
+
+ * Rebuild for Trusty
+ * Pass standard CFLAGS to build
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 07 May 2014 16:43:48 +0100
+
+sickle (0.94-0precise2) precise; urgency=low
+
+ * Fix manpage to have more useful info
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 29 Apr 2013 12:47:44 +0100
+
+sickle (0.94-0precise1) precise; urgency=low
+
+ * Initial build for PPA.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 29 Apr 2013 12:00:14 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..502e135
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: sickle
+Section: science
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: zlib1g-dev, help2man (>= 1.40.4), debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: https://github.com/vsbuffalo/sickle
+
+Package: sickle
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: windowed adaptive trimming tool for FASTQ files using quality
+ Most modern sequencing technologies produce reads that have deteriorating
+ quality towards the 3'-end. Incorrectly called bases here negatively impact
+ assembles, mapping, and downstream bioinformatics analyses.
+ .
+ Sickle is a tool that uses sliding windows along with quality and length
+ thresholds to determine when quality is sufficiently low to trim the 3'-end
+ of reads. It will also discard reads based upon the length threshold. It takes
+ the quality values and slides a window across them whose length is 0.1 times
+ the length of the read. If this length is less than 1, then the window is set
+ to be equal to the length of the read. Otherwise, the window slides along the
+ quality values until the average quality in the window drops below the
+ threshold. At that point the algorithm determines where in the window the drop
+ occurs and cuts both the read and quality strings there. However, if the cut
+ point is less than the minimum length threshold, then the read is discarded
+ entirely.
+ .
+ Sickle supports four types of quality values: Illumina, Solexa, Phred, and
+ Sanger. Note that the Solexa quality setting is an approximation (the actual
+ conversion is a non-linear transformation). The end approximation is close.
+ .
+ Sickle also supports gzipped file inputs.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..84814f3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://github.com/vsbuffalo/sickle/archive/master.zip
+License: MIT
+
+Files: *
+Copyright: © 2008 Genome Research Ltd (GRL).,
+ © 2012 - Vince Buffalo
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use, copy,
+ modify, merge, publish, distribute, sublicense, and/or sell copies
+ of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..23a7468
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+sickle usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4c07e41
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+sickle.1
diff --git a/debian/patches/makefile_ldflags b/debian/patches/makefile_ldflags
new file mode 100644
index 0000000..2f16543
--- /dev/null
+++ b/debian/patches/makefile_ldflags
@@ -0,0 +1,20 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+ PROGRAM_NAME = sickle
+ VERSION = 0.94
+ CC = gcc
+-CFLAGS = -Wall -pedantic -DVERSION=$(VERSION)
++CFLAGS += -Wall -pedantic -DVERSION=$(VERSION)
+ DEBUG = -g
+ OPT = -O3
+ ARCHIVE = $(PROGRAM_NAME)_$(VERSION)
+@@ -34,7 +34,7 @@
+ tar -zcf $(ARCHIVE).tar.gz src Makefile
+
+ build: sliding.o trim_single.o trim_paired.o sickle.o
+- $(CC) $(CFLAGS) $(LDFLAGS) $(OPT) $? -o sickle
++ $(CC) $(CFLAGS) $(OPT) $? -o sickle $(LDFLAGS)
+
+ debug:
+ $(MAKE) build "CFLAGS=-Wall -pedantic -g -DDEBUG"
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8e98eb8
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+makefile_ldflags
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..3ffb6c3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@
+
+# export DH_VERBOSE=1
+
+override_dh_clean:
+ dh_clean
+ rm -f README.help2man sickle.1
+
+override_dh_auto_build:
+ dh_auto_build
+ echo '[DESCRIPTION]' > README.help2man
+ grep -A200 '^## Usage' README.md >> README.help2man
+ help2man --no-discard-stderr -i README.help2man \
+ -n "windowed adaptive trimming tool for FASTQ files using quality" \
+ ./sickle > sickle.1
+
+get-orig-source:
+ echo Source was donloaded from GitHub. There is no script to fetch it (yet)
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
--
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