From f9dff7a99d77a60bf8c36e369bef02668495bbba Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Fri, 17 Jan 2020 12:01:19 +0100
Subject: [PATCH 1/2] cufflinks: convert to package

Rationale:

- first:
  There is no new release since ~2 years, the current
  one won't build w/o internal files from samtools'
  source tree. (Also it looks like that it needs a rather
  old version of samtools?)

- second:
  This package is the only one in the system that uses
  boost libraries, thus requiring boost to be installed
  with the library bloat.
---
 cufflinks-2.2.1-2.build.sh | 44 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100755 cufflinks-2.2.1-2.build.sh

diff --git a/cufflinks-2.2.1-2.build.sh b/cufflinks-2.2.1-2.build.sh
new file mode 100755
index 0000000..9478791
--- /dev/null
+++ b/cufflinks-2.2.1-2.build.sh
@@ -0,0 +1,44 @@
+#! /bin/sh
+
+set -xe
+
+PKG=cufflinks
+VERSION=2.2.1
+BUILD=2
+
+PKG_CUFFLINKS=/src/mariux/beeroot/packages/cufflinks-2.2.1-1.x86_64.bee.tar.bz2
+PKG_BOOST=/src/mariux/beeroot/packages/boost-1.63.0-2.x86_64.bee.tar.bz2
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
+
+mkdir -p $PREFIX
+
+cat >$PREFIX/profile <<-EOF
+	PATH=$PREFIX/bin:\$PATH
+  LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
+	if [ -d $PREFIX/.compatlibs ]; then LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
+  export LD_LIBRARY_PATH
+EOF
+
+source $PREFIX/profile
+
+mkdir -p $PREFIX/build
+cd $PREFIX/build
+
+tar -xf $PKG_CUFFLINKS /usr/bin
+mv usr/bin $PREFIX
+
+tar -xf $PKG_BOOST \
+        /usr/lib/libboost_serialization.so.1.63.0 \
+        /usr/lib/libboost_serialization.so \
+        /usr/lib/libboost_system.so.1.63.0 \
+        /usr/lib/libboost_system.so \
+        /usr/lib/libboost_thread.so.1.63.0 \
+        /usr/lib/libboost_thread.so
+mv usr/lib $PREFIX
+
+rmdir usr
+
+exit

From 58c56c8df8550fa68e767f301b46f56746a5a0cb Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Tue, 21 Jan 2020 09:33:19 +0100
Subject: [PATCH 2/2] cufflinks: Whitespace cosmetics

Approved by Cher.
---
 cufflinks-2.2.1-2.build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cufflinks-2.2.1-2.build.sh b/cufflinks-2.2.1-2.build.sh
index 9478791..1eaad80 100755
--- a/cufflinks-2.2.1-2.build.sh
+++ b/cufflinks-2.2.1-2.build.sh
@@ -17,9 +17,9 @@ mkdir -p $PREFIX
 
 cat >$PREFIX/profile <<-EOF
 	PATH=$PREFIX/bin:\$PATH
-  LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
+	LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
 	if [ -d $PREFIX/.compatlibs ]; then LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
-  export LD_LIBRARY_PATH
+	export LD_LIBRARY_PATH
 EOF
 
 source $PREFIX/profile