[med-svn] [kmer-tools] 07/13: Add leaff and sim4db binary packages

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository kmer-tools.

commit 85bd00e2a7016168f5418b6037ef0daa99fe5126
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Jan 1 22:21:30 2016 -0800

    Add leaff and sim4db binary packages
---
 debian/control        | 45 ++++++++++++++++++++++++++++++++++++++++++++-
 debian/leaff.docs     |  1 +
 debian/leaff.install  |  1 +
 debian/rules          | 13 ++++++++-----
 debian/sim4db.docs    |  1 +
 debian/sim4db.install | 27 +++++++++++++++++++++++++++
 6 files changed, 82 insertions(+), 6 deletions(-)

diff --git a/debian/control b/debian/control
index 8424146..05a9d43 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,9 @@ Package: kmer
 Architecture: any
 Depends: ${shlibs:Depends},
 	 ${misc:Depends},
-	 meryl
+	 meryl,
+	 leaff,
+	 sim4db,
 Description: suite of tools for DNA sequence analysis
  The kmer package is a suite of tools for DNA sequence analysis.
  It provides tools for searching (ESTs, mRNAs, sequencing reads);
@@ -52,6 +54,8 @@ Description: in- and out-of-core kmer counting and utilities
  report the histogram of counts, the list of kmers and their
  counts, or can perform mathematical and set operations
  on the processed data files.
+ .
+ This package is part of the Kmer suite.
 
 Package: libmeryl-dev
 Architecture: any
@@ -70,3 +74,42 @@ Description: in- and out-of-core kmer counting and utilities (development lib)
  on the processed data files.
  .
  This package contains the static libraries and header files.
+
+Package: leaff
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+Description: biological sequence library utilities and applications
+ LEAFF (Let's Extract Anything From Fasta) is a utility program for
+ working with multi-fasta files. In addition to providing random access
+ to the base level, it includes several analysis functions.
+ .
+ This package is part of the Kmer suite.
+
+Package: sim4db
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+Recommends:
+	leaff,
+Description: biological sequence library utilities and applications
+ Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
+ sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
+ algorithms to determine the alignments, but incorporates a fast sequence
+ indexing and retrieval mechanism, implemented in the sister package
+ 'leaff', to speedily process large volumes of sequences.
+ .
+ While sim4db produces alignments in the same way as sim4 or sim4cc, it
+ has additional features to make it more amenable for use with whole-genome
+ annotation pipelines. A script file can be used to group pairings between
+ cDNAs and their corresponding genomic regions, to be aligned as one run
+ and using the same set of parameters. Sim4db also optionally reports more
+ than one alignment for the same cDNA within a genomic region, as long
+ as they meet user-defined criteria such as minimum length, percentage
+ sequence identity or coverage. This feature is instrumental in finding
+ all alignments of a gene family at one locus. Lastly, the output is
+ presented either as custom sim4db alignments or as GFF3 gene features.
+ .
+ This package is part of the Kmer suite.
diff --git a/debian/leaff.docs b/debian/leaff.docs
new file mode 100644
index 0000000..e50f353
--- /dev/null
+++ b/debian/leaff.docs
@@ -0,0 +1 @@
+README.leaff
diff --git a/debian/leaff.install b/debian/leaff.install
new file mode 100644
index 0000000..341d21a
--- /dev/null
+++ b/debian/leaff.install
@@ -0,0 +1 @@
+installdir/bin/leaff usr/bin
diff --git a/debian/rules b/debian/rules
index 63d2482..d168a9d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,7 +9,10 @@ CXXFLAGS:=$(CPPFLAGS) $(CXXFLAGS)
 
 # The trailing slashes are very important to the build system
 subdirectories:= $(filter-out debian/, $(shell ls -d */))
-meryl:= libbio/ libkmer/ libmeryl/ libseq/ libutil/ meryl/
+
+# Reference for unusable modules:
+# https://lists.debian.org/debian-med/2015/05/msg00075.html
+unusable:= tapper/ trie/
 
 %:
 	dh $@ 
@@ -18,10 +21,10 @@ override_dh_auto_build:
         # The Makefile apparently doesn't use regular LDFLAGS.
         # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's
         # use them here.
-	$(MAKE) \
-            CLDFLAGS="$(LDFLAGS)" \
-            CXXLDFLAGS="$(LDFLAGS)" \
-            WITHOUT="$(filter-out $(meryl), $(subdirectories))" install
+	$(MAKE) install \
+	    CLDFLAGS="$(LDFLAGS)" \
+	    CXXLDFLAGS="$(LDFLAGS)"
+#	    WITHOUT="$(unusable)"
 	ln -sf $(shell uname)-* installdir
 
 override_dh_auto_clean:
diff --git a/debian/sim4db.docs b/debian/sim4db.docs
new file mode 100644
index 0000000..2d7c735
--- /dev/null
+++ b/debian/sim4db.docs
@@ -0,0 +1 @@
+README.sim4db
diff --git a/debian/sim4db.install b/debian/sim4db.install
new file mode 100644
index 0000000..d9b3961
--- /dev/null
+++ b/debian/sim4db.install
@@ -0,0 +1,27 @@
+installdir/bin/sim4db	usr/bin
+# sim4dbutils
+installdir/bin/filterPolishes	usr/bin
+installdir/bin/headPolishes	usr/bin
+installdir/bin/mappedCoverage	usr/bin
+installdir/bin/mergePolishes	usr/bin
+installdir/bin/sortPolishes	usr/bin
+installdir/bin/pickBestPolish	usr/bin
+installdir/bin/pickBestPair	usr/bin
+installdir/bin/pickUniquePolish	usr/bin
+installdir/bin/cleanPolishes	usr/bin
+installdir/bin/fixPolishesIID	usr/bin
+installdir/bin/plotCoverageVsIdentity	usr/bin
+installdir/bin/parseSNP	usr/bin
+installdir/bin/comparePolishes	usr/bin
+installdir/bin/convertToAtac	usr/bin
+installdir/bin/convertToExtent	usr/bin
+installdir/bin/convertPolishes	usr/bin
+installdir/bin/depthOfPolishes	usr/bin
+installdir/bin/detectChimera	usr/bin
+installdir/bin/uniqPolishes	usr/bin
+installdir/bin/summarizePolishes	usr/bin
+installdir/bin/removeDuplicate	usr/bin
+installdir/bin/vennPolishes	usr/bin
+installdir/bin/realignPolishes	usr/bin
+installdir/bin/removeRedundant	usr/bin
+installdir/bin/reportAlignmentDifferences	usr/bin

-- 
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