initial working commit

5 files changed, 40 insertions, 11 deletions

diff --git a/.SRCINFO b/.SRCINFO
index c7700747c3f3..5e86fbd3fb22 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,20 +1,23 @@
 # Generated by mksrcinfo v8
-# Wed Jan 20 11:31:34 UTC 2016
+# Wed Jan 20 15:38:04 UTC 2016
 pkgbase = homer
 	pkgdesc = Hypergeometric Optimization of Motif EnRichment
 	pkgver = 4.8
 	pkgrel = 1
 	url = http://homer.salk.edu/
+	install = homer.install
 	arch = i686
 	arch = x86_64
 	license = GPLv3
 	depends = perl
-	depends = weblogo
+	depends = weblogo2
 	depends = wget
 	optdepends = ucsc-kent-genome-tools: for the blat tool, required for removing redundant sequences during motif finding
 	optdepends = ghostscript: required for making motif logos
-	source = http://homer.salk.edu/homer/configureHomer.pl
-	md5sums = f0f52cfe22bfe341532a11d947aac803
+	source = http://homer.salk.edu/homer/data/software/homer.v4.8.zip
+	source = homer.sh
+	md5sums = 173c9ad0e35d7639b89331de87505928
+	md5sums = 81a149ed531dcca7f0096901fd88ddeb
 
 pkgname = homer
 
diff --git a/.gitignore b/.gitignore
index 3ea950438567..d060381623c1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@
 pkg/
 src/
 *.pl
+*.zip
diff --git a/PKGBUILD b/PKGBUILD
index 473e8b21ca75..5b856392f3f9 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -9,21 +9,41 @@ arch=('i686' 'x86_64')
 license=('GPLv3')
 optdepends=('ucsc-kent-genome-tools: for the blat tool, required for removing redundant sequences during motif finding'
   'ghostscript: required for making motif logos')
-depends=('perl' 'weblogo' 'wget')
-source=("http://homer.salk.edu/homer/configureHomer.pl")
-md5sums=('f0f52cfe22bfe341532a11d947aac803')
-#options=(!strip docs libtool emptydirs !zipman staticlibs !upx)
+depends=('perl' 'weblogo2' 'wget')
+source=("http://homer.salk.edu/homer/data/software/homer.v${pkgver}.zip" "homer.sh")
+md5sums=('173c9ad0e35d7639b89331de87505928'
+         '81a149ed531dcca7f0096901fd88ddeb')
+install=('homer.install')
 
 prepare(){
-msg "preparing"
+  cd ${srcdir}/cpp
+  make clean
 }
 
 build(){
-msg "building"
+  #cd ${srcdir}
+  #perl configureHomer.pl -install homer
+
+  cd ${srcdir}/cpp
+  make # this actually also copies the exes to bin/ then clean can't clean them
+  make clean
 }
 
 package() {
-msg "packaging"
+  # just put everything into opt
+  mkdir -p "${pkgdir}/opt/${pkgname}"
+  cp -a ${srcdir}/* "${pkgdir}/opt/${pkgname}/."
+
+  # link the main perl script
+  mkdir -p ${pkgdir}/usr/bin
+  chmod 755 "${pkgdir}/opt/${pkgname}/configureHomer.pl"
+  ln -s /opt/${pkgname}/configureHomer.pl ${pkgdir}/usr/bin/.
+
+  # install profile file
+  install -m755 -D "${srcdir}/homer.sh" -t "${pkgdir}/etc/profile.d"
+  
+  # install license file
+  install -m644 -D "${srcdir}/COPYING" -t "${pkgdir}/usr/share/licenses/${pkgname}"
 }
 
 # vim:set ts=2 sw=2 et:#
diff --git a/homer.install b/homer.install
new file mode 100644
index 000000000000..5ac33ab1ec23
--- /dev/null
+++ b/homer.install
@@ -0,0 +1,3 @@
+post_install() {
+  source /etc/profile
+}
diff --git a/homer.sh b/homer.sh
new file mode 100755
index 000000000000..e3a6f225d82c
--- /dev/null
+++ b/homer.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+PATH="$PATH:/opt/homer/bin"