[med-svn] [kmer] 01/01: (WIP) new binary package - estmapper
Afif Elghraoui
afif at moszumanska.debian.org
Sun Dec 4 05:50:46 UTC 2016
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afif pushed a commit to branch topic/estmapper
in repository kmer.
commit 10a63d2a78e3eb3a9d85f388d4e8478fd005dfd2
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Wed Nov 30 02:17:09 2016 -0800
(WIP) new binary package - estmapper
Testing using the steps at
<http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ESTmapper>,
there is a memory error when calling seagen. I attempted
compiling with -std=c+=98, but this did not help.
---
debian/control | 19 ++++++
debian/estmapper.install | 16 +++++
debian/patches/estmapper-helper-script-paths.patch | 75 ++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 1 +
5 files changed, 112 insertions(+)
diff --git a/debian/control b/debian/control
index 6f8ec94..c3c0053 100644
--- a/debian/control
+++ b/debian/control
@@ -115,6 +115,25 @@ Description: batch spliced alignment of cDNA sequences to a target genome
.
This package is part of the Kmer suite.
+Package: estmapper
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends},
+ libfile-which-perl,
+ meryl,
+ leaff,
+ sim4db,
+Suggests: gridengine-client
+Description: biological sequence library utilities and applications
+ ESTmapper is a software package for the high-throughput alignment of large
+ cDNA (EST, mRNA) sequence sets to a large eukaryotic genome of the same
+ species. It can also be used to map relatively short DNA segments, such as
+ sequencing reads or SNP flanking sequences, to the genome.
+ .
+ This package is part of the Kmer suite.
+
Package: atac
Architecture: any
Depends:
diff --git a/debian/estmapper.install b/debian/estmapper.install
new file mode 100644
index 0000000..329d7f9
--- /dev/null
+++ b/debian/estmapper.install
@@ -0,0 +1,16 @@
+installdir/bin/ESTmapper.pl /usr/bin
+installdir/bin/configureESTmapper.pl /usr/bin
+installdir/bin/runConcurrently.pl /usr/lib/estmapper/bin
+installdir/bin/mergeCounts /usr/lib/estmapper/bin
+installdir/bin/terminate /usr/lib/estmapper/bin
+installdir/lib/scheduler.pm /usr/lib/estmapper/lib
+
+# From seagen/
+installdir/bin/seagen /usr/lib/estmapper/bin
+installdir/bin/hitConverter /usr/lib/estmapper/bin
+installdir/bin/filterEST /usr/lib/estmapper/bin
+installdir/bin/filterMRNA /usr/lib/estmapper/bin
+installdir/bin/filterNULL /usr/lib/estmapper/bin
+installdir/bin/filtertest /usr/lib/estmapper/bin
+installdir/bin/sortHits /usr/lib/estmapper/bin
+installdir/bin/filterESTsimple /usr/lib/estmapper/bin
diff --git a/debian/patches/estmapper-helper-script-paths.patch b/debian/patches/estmapper-helper-script-paths.patch
new file mode 100644
index 0000000..87ac86e
--- /dev/null
+++ b/debian/patches/estmapper-helper-script-paths.patch
@@ -0,0 +1,75 @@
+Description: Adjust paths to private executables for estmapper
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-11-30
+--- kmer-tools.orig/ESTmapper/ESTmapper.pl
++++ kmer-tools/ESTmapper/ESTmapper.pl
+@@ -9,9 +9,10 @@
+ # Perl version 5.005_03 is too old, it requires two args to mkdir.
+
+ use strict;
++use File::Which;
+ use FindBin;
+ use Config; # for @signame
+-use lib "$FindBin::Bin/../lib";
++use lib "$FindBin::Bin/../lib/estmapper/lib";
+
+ use scheduler;
+
+@@ -82,24 +83,24 @@
+
+
+ sub setExecutables {
+- my $exechome = "$FindBin::Bin";
++ my $exechome = "$FindBin::Bin/../lib/estmapper/bin";
+
+- $prog{'ESTmapper'} = "$exechome/ESTmapper.pl";
++ $prog{'ESTmapper'} = which("ESTmapper.pl");
+ $prog{'seagen'} = "$exechome/seagen";
+ $prog{'mergeCounts'} = "$exechome/mergeCounts";
+ $prog{'filterEST'} = "$exechome/filterEST";
+ $prog{'filterMRNA'} = "$exechome/filterMRNA";
+ $prog{'filterNULL'} = "$exechome/filterNULL";
+- $prog{'sim4db'} = "$exechome/sim4db";
+- $prog{'leaff'} = "$exechome/leaff";
+- $prog{'meryl'} = "$exechome/meryl";
+- $prog{'cleanPolishes'} = "$exechome/cleanPolishes";
+- $prog{'toFILTER'} = "$exechome/filterPolishes";
++ $prog{'sim4db'} = which("sim4db");
++ $prog{'leaff'} = which("leaff");
++ $prog{'meryl'} = which("meryl");
++ $prog{'cleanPolishes'} = which("cleanPolishes");
++ $prog{'toFILTER'} = which("filterPolishes");
+ $prog{'sortHits'} = "$exechome/sortHits";
+- $prog{'sortPolishes'} = "$exechome/sortPolishes";
+- $prog{'parseSNPs'} = "$exechome/parseSNP";
+- $prog{'pickBest'} = "$exechome/pickBestPolish";
+- $prog{'positionDB'} = "$exechome/positionDB";
++ $prog{'sortPolishes'} = which("sortPolishes");
++ $prog{'parseSNPs'} = which("parseSNP");
++ $prog{'pickBest'} = which("pickBestPolish");
++ $prog{'positionDB'} = which("positionDB");
+ $prog{'terminate'} = "$exechome/terminate";
+
+ foreach my $e (keys %prog) {
+--- kmer-tools.orig/ESTmapper/configureESTmapper.pl
++++ kmer-tools/ESTmapper/configureESTmapper.pl
+@@ -1,14 +1,14 @@
+ #!/usr/bin/perl
+
+ use strict;
++use File::Which;
+ use FindBin;
+ use Config; # for @signame
+ use lib "$FindBin::Bin/util";
+
+-my $exechome = "$FindBin::Bin";
+-my $leaff = "$exechome/leaff";
+-my $posdb = "$exechome/positionDB";
+-my $meryl = "$exechome/meryl";
++my $leaff = which("leaff");
++my $posdb = which("positionDB");
++my $meryl = which("meryl");
+
+ my $genome = undef;
+ my $genomedir = undef;
diff --git a/debian/patches/series b/debian/patches/series
index a717064..e36ba5e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
allow-freebsd-build.patch
atac-helper-script-paths.patch
atac-readme.patch
+estmapper-helper-script-paths.patch
diff --git a/debian/rules b/debian/rules
index a7af23d..11c745b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,7 @@
#!/usr/bin/make -f
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_CXXFLAGS_MAINT_APPEND = -std=c++98
DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/default.mk
--
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