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'Add ddocent: Bash pipeline for ddRAD sequencing'
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon@centosdev.local>
Pushed By: outpaddling
Date: Thu Mar 30 20:38:36 2017 -0500
Changeset: bebb209559ff34f08ab0ed4e20d759cbd5896bac
Modified Files:
Makefile
Added Files:
ddocent/DESCR
ddocent/Makefile
ddocent/PLIST
ddocent/TODO
ddocent/buildlink3.mk
ddocent/distinfo
ddocent/patches/patch-dDocent
Log Message:
'Add ddocent: Bash pipeline for ddRAD sequencing'
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=bebb209559ff34f08ab0ed4e20d759cbd5896bac
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
ddocent/DESCR | 1 +
ddocent/Makefile | 56 +++++++++++++++++++++++++++++++++++++++++++
ddocent/PLIST | 11 +++++++++
ddocent/TODO | 1 +
ddocent/buildlink3.mk | 12 ++++++++++
ddocent/distinfo | 7 ++++++
ddocent/patches/patch-dDocent | 24 +++++++++++++++++++
8 files changed, 113 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index f4b3fa419b..e054eaa3ff 100644
--- a/Makefile
+++ b/Makefile
@@ -477,6 +477,7 @@ SUBDIR+= dbf
SUBDIR+= dbus-dfbsd
SUBDIR+= dbus-explorer
SUBDIR+= ddate
+SUBDIR+= ddocent
SUBDIR+= deadbeef
SUBDIR+= debian_base
SUBDIR+= debian_glib
diff --git a/ddocent/DESCR b/ddocent/DESCR
new file mode 100644
index 0000000000..845dbab1b0
--- /dev/null
+++ b/ddocent/DESCR
@@ -0,0 +1 @@
+[description of the port]
diff --git a/ddocent/Makefile b/ddocent/Makefile
new file mode 100644
index 0000000000..ac7cdaa1f6
--- /dev/null
+++ b/ddocent/Makefile
@@ -0,0 +1,56 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+###########################################################
+
+DISTNAME= ddocent-${PORTVERSION}
+CATEGORIES= biology
+MASTER_SITES= http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX= .tar.xz
+PKGNAME= ddocent-${PORTVERSION}
+
+MAINTAINER= dsiercks%uwm.edu@localhost
+HOMEPAGE= http://ddocent.wordpress.com/
+COMMENT= Bash pipeline for ddRAD sequencing
+LICENSE= mit
+
+NO_BUILD= yes
+
+REPLACE_BASH= scripts/*.sh scripts/dDocent_filters
+REPLACE_PERL= scripts/*.pl
+
+PORTVERSION= 2015.11.30
+
+# This subst is applied on top of patch-dDocent
+# Do not apply it within the source dist, or it will get picked up
+# next time the patch is generated with pkg-diff or mkpatches
+SUBST_CLASSES+= prefix
+SUBST_STAGE.prefix= post-install
+SUBST_FILES.prefix= ${DESTDIR}${PREFIX}/bin/dDocent
+SUBST_SED.prefix= -e 's|%%PREFIX%%|${PREFIX}|g'
+
+DEPENDS+= gnuplot>=3.7:../../graphics/gnuplot \
+ cdhit>=4.6:../../biology/cdhit \
+ parallel>=0:../../wip/parallel \
+ gawk>=0:../../lang/gawk \
+ vcftools>=0.1.11:../../wip/vcftools \
+ stacks>=0:../../wip/stacks \
+ Trimmomatic:../../wip/trimmomatic \
+ seqtk>=0:../../wip/seqtk \
+ bedtools2>=2.23.0:../../wip/bedtools2 \
+ pear-merger>=0:../../wip/pear \
+ mawk>=0:../../lang/mawk
+
+INSTALLATION_DIRS= bin
+
+do-install:
+ ${INSTALL_SCRIPT} \
+ ${WRKSRC}/dDocent \
+ ${WRKSRC}/scripts/* ${DESTDIR}${PREFIX}/bin
+
+.include "../../wip/bamtools/buildlink3.mk"
+.include "../../wip/freebayes/buildlink3.mk"
+.include "../../wip/samtools0119/buildlink3.mk"
+.include "../../wip/vcflib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/ddocent/PLIST b/ddocent/PLIST
new file mode 100644
index 0000000000..722b91fc7e
--- /dev/null
+++ b/ddocent/PLIST
@@ -0,0 +1,11 @@
+@comment $NetBSD$
+bin/dDocent
+bin/dDocent_filters
+bin/ErrorCount.sh
+bin/filter_hwe_by_pop.pl
+bin/filter_missing_ind.sh
+bin/pop_missing_filter.sh
+bin/ReferenceOpt.sh
+bin/remake_reference.sh
+bin/remove.bad.hap.loci.sh
+bin/Rename_SequenceFiles.sh
diff --git a/ddocent/TODO b/ddocent/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/ddocent/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/ddocent/buildlink3.mk b/ddocent/buildlink3.mk
new file mode 100644
index 0000000000..b82245f541
--- /dev/null
+++ b/ddocent/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+= ddocent
+
+.if !defined(DDOCENT_BUILDLINK3_MK)
+DDOCENT_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.ddocent+= ddocent>=2015.11.30
+BUILDLINK_PKGSRCDIR.ddocent?= ../../wip/ddocent
+.endif # DDOCENT_BUILDLINK3_MK
+
+BUILDLINK_TREE+= -ddocent
diff --git a/ddocent/distinfo b/ddocent/distinfo
new file mode 100644
index 0000000000..e7166015fa
--- /dev/null
+++ b/ddocent/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (ddocent-2015.11.30.tar.xz) = f28e87ae4b4c26d5a771f71cb05e5ba03433d7ee
+RMD160 (ddocent-2015.11.30.tar.xz) = e1b45882d611208bdf68badae4bd9a7e93ecae05
+SHA512 (ddocent-2015.11.30.tar.xz) = a19751347fa503351182260bff2688e89c418f6f62e5de63658df6e90a4ecf7dae1d677b7416332ba61335ad04a0203b788c43e8b392f61fb40be20bd5b3b102
+Size (ddocent-2015.11.30.tar.xz) = 47672 bytes
+SHA1 (patch-dDocent) = f7de578aa81fcd0680a9b221bf47cdd44b353763
diff --git a/ddocent/patches/patch-dDocent b/ddocent/patches/patch-dDocent
new file mode 100644
index 0000000000..aa59eb91ab
--- /dev/null
+++ b/ddocent/patches/patch-dDocent
@@ -0,0 +1,24 @@
+$NetBSD$
+
+--- dDocent.orig 2015-11-30 19:35:04.016417718 -0600
++++ dDocent 2015-11-30 19:40:47.765418264 -0600
+@@ -27,15 +27,15 @@ do
+ fi
+ done
+
+-if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null| grep -q 'trim' ; then
+- TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
++if [ -e %%PREFIX%%/lib/java/trimmomatic-0.35.jar ]; then
++ TRIMMOMATIC=%%PREFIX%%/lib/java/trimmomatic-0.35.jar
+ else
+ echo "The dependency trimmomatic is not installed or is not in your" '$PATH'"."
+ NUMDEP=$((NUMDEP + 1))
+ fi
+
+-if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | grep -q 'Tru' ; then
+- ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
++if [ -e %%PREFIX%%/share/Trimmomatic/adapters/TruSeq2-PE.fa ]; then
++ ADAPTERS=%%PREFIX%%/share/Trimmomatic/adapters/TruSeq2-PE.fa
+ else
+ echo "The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
+ NUMDEP=$((NUMDEP + 1))
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