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-rw-r--r--sci-biology/staden/Manifest9
-rw-r--r--sci-biology/staden/files/Makefile.in.patch11
-rw-r--r--sci-biology/staden/files/ax_lib_samtools.m4.patch34
-rw-r--r--sci-biology/staden/files/configure.patch11
-rw-r--r--sci-biology/staden/files/course_unix.texinfo.patch12
-rw-r--r--sci-biology/staden/files/destdir.patch15
-rw-r--r--sci-biology/staden/files/destdir2.patch131
-rw-r--r--sci-biology/staden/files/man-init-tar.patch14
-rw-r--r--sci-biology/staden/files/staden-src-1-7-0.patch2270
-rw-r--r--sci-biology/staden/files/system.mk.in.patch31
10 files changed, 538 insertions, 0 deletions
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index 6a1426723..5276e3e20 100644
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,3 +1,12 @@
+AUX Makefile.in.patch 312 RMD160 3640a8a6ed6ec44603e188f951ffecf6b3d01fe7 SHA1 406cd003a443a9e890837dbcf425809a5ec09a51 SHA256 805a4ea1770bfbaee641294b1c94e571474ce5711410c3850dbbb465cb31d5f6
+AUX ax_lib_samtools.m4.patch 1482 RMD160 c6448b892a29c5d7cd5f00213cecfd18a2d47bcb SHA1 da572f526a866a491e3af55fddd84a65264b0631 SHA256 75d76322a4e622f7964538241da9039c8b91b2957441db2c06a1ec3c35bcf2ce
+AUX configure.patch 422 RMD160 14dc334ac9aa83c73dc04a361fc4cecfc1f6349d SHA1 18d48e9cd78403c0615089fbf1b5e302d7a6c9c6 SHA256 8e64992d65d236b306e8d110eca8387a158b2c328aca380aa736ce5e6d878648
+AUX course_unix.texinfo.patch 338 RMD160 333d24108e23e5e18a384ff3c1f7dd44d31a4f87 SHA1 674f834856876eb9cce3b6ac7ba7ebb271d739b5 SHA256 96b808faf9055d887e22b2a2e58b1e948b1a19424b69dbec5d2c87454626df85
+AUX destdir.patch 520 RMD160 1b7f687639a0a4bf6d833a08f0d2588bda7dd4d2 SHA1 d20be03a9e1edea24466034135cead570454a29a SHA256 de2b23dc82fab5fb438a5254e874490e182cddbf83a8f28eba4c17fab4d9c472
+AUX destdir2.patch 5119 RMD160 c7e19b944dd621178d439312d999ac8d27ef44d4 SHA1 252e128cfa5da556c21ef2d823a38ac78b1cf068 SHA256 c0b23eaa0350ac314f2930a3e0b4028ae4fd28e48e2a850cd85007c2cd9576af
+AUX man-init-tar.patch 337 RMD160 666461c23ffb19a4fd6aa8d6fd0c8c696a2ab220 SHA1 583a35a2f983fdff1d8800bccb723dbd994990a4 SHA256 b26a8403bb06a52bb9bba6544b8cbdf8d75b67a190ec09441228a79887a8352e
+AUX staden-src-1-7-0.patch2 8841 RMD160 9f8784793a402fe3a6a47ca7e967a3e913ae8993 SHA1 cce4e8770011065e88d55693c776a5d05bcc5a34 SHA256 b4286bbb17bbf72973614bf6a1a15ff25be19252a79fdb3a26b5004fed4b6a8f
+AUX system.mk.in.patch 1193 RMD160 cd67adaea4c8ae85bdef1addce13b3fc1413eaf8 SHA1 b1d97579b0e41c8f9206452430e7f7c733171069 SHA256 ac26beefcca0d4977a6a144afa290c3ad0f73dbe954ed2dbbef8347ebbf25d48
DIST staden-2.0.0b7-src.tar.gz 27414341 RMD160 453c0879e82fd6d445dff2ccb7747e0cd56158a4 SHA1 02fd09715acca0b31f4bb9f1a67ce4e204d9a20b SHA256 c8b293a72e63d6ccc05209ed0200e8bc3d75df6a6e44eb02aecb4713274a6034
EBUILD staden-2.0.0.ebuild 1600 RMD160 124e220dacfaa58e265e3549e61be02a34cdcdb5 SHA1 0469fcbcbe07c48f46c7dbb275bfbf33cd62b90e SHA256 6defa2558e75a0a9f377439119b9ab3fd0d90c3ada3eb95eed8c7ec8d1136c81
EBUILD staden-9999.ebuild 2296 RMD160 5c482ced1b8af966e9265939d487dd326f58097d SHA1 b9bc920e6e6966b0e294ce7e92fd41cc942fde0b SHA256 b9619da1bdd0b45b7a8461560e109e62f016416026ab4773c67fcbd64c42a906
diff --git a/sci-biology/staden/files/Makefile.in.patch b/sci-biology/staden/files/Makefile.in.patch
new file mode 100644
index 000000000..2d96b0cd3
--- /dev/null
+++ b/sci-biology/staden/files/Makefile.in.patch
@@ -0,0 +1,11 @@
+--- staden-2.0.0b7-src/Makefile.in 2010-08-02 13:26:53.000000000 +0200
++++ staden-2.0.0b7-src/Makefile.in 2010-08-02 13:27:37.000000000 +0200
+@@ -209,7 +209,7 @@
+ haplo: gap4
+ prefinish: gap4
+ tgap: seq_utils
+-gap5: tgap
++gap5: tgap primer3/src
+
+ FORCE:
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
diff --git a/sci-biology/staden/files/ax_lib_samtools.m4.patch b/sci-biology/staden/files/ax_lib_samtools.m4.patch
new file mode 100644
index 000000000..243d2edc3
--- /dev/null
+++ b/sci-biology/staden/files/ax_lib_samtools.m4.patch
@@ -0,0 +1,34 @@
+--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/01/14 12:14:01 1949
++++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/08/02 09:20:59 2190
+@@ -117,7 +117,8 @@
+ if test "x$SAMTOOLS_ROOT" == "x"
+ then
+ samtools_exe=samtools
+- elseif test -x "$SAMTOOLS_ROOT/bin/samtools"
++ elif test -x "$SAMTOOLS_ROOT/bin/samtools"
++ then
+ samtools_exe="$SAMTOOLS_ROOT/bin/samtools"
+ else
+ samtools_exe="$SAMTOOLS_ROOT/samtools"
+--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/08/02 09:20:59 2190
++++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/08/02 11:12:53 2192
+@@ -6,7 +6,7 @@
+ #
+ # This macro will check for the existence of samtools 'bam' library.
+ # (http://samtools.sourceforge.net/). It does this by checking for the
+-# header file ibam.h and the bam library object file. These are
++# header file bam.h and the bam library object file. These are
+ # initially searched for in the include and lib subdirectory of the
+ # --with-samtools=DIR, and if not found there directly within DIR
+ # itself. This allows for --with-samtools to be specified as either
+--- staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/08/02 11:12:53 2192
++++ staden/trunk/src/ac_stubs/ax_lib_samtools.m4 2010/08/02 11:23:16 2193
+@@ -99,7 +99,7 @@
+
+ if test "$samtools_ok" = "yes"
+ then
+- SAMTOOLS_LDFLAGS="$ZLIB_LDFLAGS"
++ SAMTOOLS_LDFLAGS="-lbam $ZLIB_LDFLAGS"
+ SAMTOOLS_CFLAGS=
+ fi
+ fi
diff --git a/sci-biology/staden/files/configure.patch b/sci-biology/staden/files/configure.patch
new file mode 100644
index 000000000..44d42ad50
--- /dev/null
+++ b/sci-biology/staden/files/configure.patch
@@ -0,0 +1,11 @@
+--- configure 2010-07-15 13:36:13.000000000 +0200
++++ /tmp/configure 2010-08-02 10:35:08.000000000 +0200
+@@ -6693,7 +6693,7 @@
+ if test "x$SAMTOOLS_ROOT" == "x"
+ then
+ samtools_exe=samtools
+- elseif test -x "$SAMTOOLS_ROOT/bin/samtools"
++ elif test -x "$SAMTOOLS_ROOT/bin/samtools"; then
+ samtools_exe="$SAMTOOLS_ROOT/bin/samtools"
+ else
+ samtools_exe="$SAMTOOLS_ROOT/samtools"
diff --git a/sci-biology/staden/files/course_unix.texinfo.patch b/sci-biology/staden/files/course_unix.texinfo.patch
new file mode 100644
index 000000000..e3ee8cebc
--- /dev/null
+++ b/sci-biology/staden/files/course_unix.texinfo.patch
@@ -0,0 +1,12 @@
+--- course/texi/Makefile.ori 2009-02-23 03:48:35.000000000 +0100
++++ course/texi/Makefile 2009-02-23 03:48:49.000000000 +0100
+@@ -55,7 +55,7 @@
+ #-----------------------------------------------------------------------------
+ # The main make targets.
+
+-all: unix windows
++all: windows
+
+ unix: course_unix.ps course_unix.pdf
+
+
diff --git a/sci-biology/staden/files/destdir.patch b/sci-biology/staden/files/destdir.patch
new file mode 100644
index 000000000..72f1bd8d7
--- /dev/null
+++ b/sci-biology/staden/files/destdir.patch
@@ -0,0 +1,15 @@
+Index: system.mk.in
+===================================================================
+--- system.mk.in (revision 2189)
++++ system.mk.in (working copy)
+@@ -113,8 +113,8 @@
+
+ # Our libraries are I think exclusively used by us, hence we pick
+ # our own subdirectory.
+-prefix = @prefix@
+-exec_prefix = @exec_prefix@
++prefix = ${DESTDIR}@prefix@
++exec_prefix = ${DESTDIR}@exec_prefix@
+ INSTALLLIB = @libdir@/staden
+ INSTALLBIN = @bindir@
+ #INSTALLETC = @sysconfdir@/staden
diff --git a/sci-biology/staden/files/destdir2.patch b/sci-biology/staden/files/destdir2.patch
new file mode 100644
index 000000000..418dfc34f
--- /dev/null
+++ b/sci-biology/staden/files/destdir2.patch
@@ -0,0 +1,131 @@
+--- Makefile.in.ori 2010-08-06 14:09:46.000000000 +0200
++++ Makefile.in 2010-08-06 14:13:03.000000000 +0200
+@@ -70,16 +70,16 @@
+ # Installs newly built executables into $STADENROOT/$(MACHINE)-bin
+ # FIXME:
+ install:
+- -mkdir -p $(INSTALLLIB)
+- -mkdir -p $(INSTALLBIN)
+- -mkdir -p $(INSTALLETC)
+- -mkdir -p $(INSTALLSHARE)
+- -mkdir -p $(INSTALLSCRIPTS)
+- -mkdir -p $(INSTALLTCL)
+- -mkdir -p $(INSTALLDOC)
+- -mkdir -p $(INSTALLMAN)
+- cp shlib.conf $(INSTALLETC)
+- cp @srcdir@/staden.profile $(INSTALLSHARE)
++ -mkdir -p $(DESTDIR)$(INSTALLLIB)
++ -mkdir -p $(DESTDIR)$(INSTALLBIN)
++ -mkdir -p $(DESTDIR)$(INSTALLETC)
++ -mkdir -p $(DESTDIR)$(INSTALLSHARE)
++ -mkdir -p $(DESTDIR)$(INSTALLSCRIPTS)
++ -mkdir -p $(DESTDIR)$(INSTALLTCL)
++ -mkdir -p $(DESTDIR)$(INSTALLDOC)
++ -mkdir -p $(DESTDIR)$(INSTALLMAN)
++ cp shlib.conf $(DESTDIR)$(INSTALLETC)
++ cp @srcdir@/staden.profile $(DESTDIR)$(INSTALLSHARE)
+ $(MAKE) $(FLAGS) JOB=install
+
+
+@@ -95,35 +95,35 @@
+ # and will be copied over separately. This is because in some cases they will
+ # have been manually hacked/bug fixed.
+ distunix:
+- -mkdir $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libpng* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libtcl* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libtk* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libitcl* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libitk* $(DIST)/lib/$(MACHINE)-binaries
++ -mkdir $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
++ -cp -R lib/$(MACHINE)-binaries/libpng* $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
++ -cp -R lib/$(MACHINE)-binaries/libtcl* $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
++ -cp -R lib/$(MACHINE)-binaries/libtk* $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
++ -cp -R lib/$(MACHINE)-binaries/libitcl* $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
++ -cp -R lib/$(MACHINE)-binaries/libitk* $(DESTDIR)$(DIST)/lib/$(MACHINE)-binaries
+
+
+ distwindows:
+- -mkdir $(DIST)/lib/windows-binaries
+- -cp lib/windows-binaries/* $(DIST)/lib/windows-binaries
+- -cp windows/run/sprun.exe $(DIST)/windows-bin/
+- -cp windows/run/sprun.exe $(DIST)/windows-bin/gap.exe
+- -cp windows/run/sprun.exe $(DIST)/windows-bin/pregap4.exe
+- -cp windows/run/sprun.exe $(DIST)/windows-bin/spin.exe
+- -cp windows/run/sprun.exe $(DIST)/windows-bin/trev.exe
+- -cp tk8.4.6/win/wish84.exe $(DIST)/windows-bin/wish.exe
+- #-cp trev/trev.bat $(DIST)/windows-bin
+- #-cp gap4/gap4.bat $(DIST)/windows-bin
+- #-cp spin/spin.bat $(DIST)/windows-bin
+- #-cp pregap4/pregap4.bat $(DIST)/windows-bin
+- -cp ../windows-bin/*.exe $(DIST)/windows-bin
++ -mkdir $(DESTDIR)$(DIST)/lib/windows-binaries
++ -cp lib/windows-binaries/* $(DESTDIR)$(DIST)/lib/windows-binaries
++ -cp windows/run/sprun.exe $(DESTDIR)$(DIST)/windows-bin/
++ -cp windows/run/sprun.exe $(DESTDIR)$(DIST)/windows-bin/gap.exe
++ -cp windows/run/sprun.exe $(DESTDIR)$(DIST)/windows-bin/pregap4.exe
++ -cp windows/run/sprun.exe $(DESTDIR)$(DIST)/windows-bin/spin.exe
++ -cp windows/run/sprun.exe $(DESTDIR)$(DIST)/windows-bin/trev.exe
++ -cp tk8.4.6/win/wish84.exe $(DESTDIR)$(DIST)/windows-bin/wish.exe
++ #-cp trev/trev.bat $(DESTDIR)$(DIST)/windows-bin
++ #-cp gap4/gap4.bat $(DESTDIR)$(DIST)/windows-bin
++ #-cp spin/spin.bat $(DESTDIR)$(DIST)/windows-bin
++ #-cp pregap4/pregap4.bat $(DESTDIR)$(DIST)/windows-bin
++ -cp ../windows-bin/*.exe $(DESTDIR)$(DIST)/windows-bin
+ $(MAKE) STADENROOT=$(DIST) MACHINE=windows install
+- -rm $(DIST)/windows-bin/gap4
+- -rm $(DIST)/windows-bin/spin
+- -rm $(DIST)/windows-bin/trev
+- -rm $(DIST)/windows-bin/pregap4
+- -rm $(DIST)/windows-bin/assemble4
+- -rm $(DIST)/windows-bin/finish_sanger
++ -rm $(DESTDIR)$(DIST)/windows-bin/gap4
++ -rm $(DESTDIR)$(DIST)/windows-bin/spin
++ -rm $(DESTDIR)$(DIST)/windows-bin/trev
++ -rm $(DESTDIR)$(DIST)/windows-bin/pregap4
++ -rm $(DESTDIR)$(DIST)/windows-bin/assemble4
++ -rm $(DESTDIR)$(DIST)/windows-bin/finish_sanger
+
+
+
+@@ -132,10 +132,10 @@
+ distsrc:
+ #
+ # General souce. Works best from a clean svn checkout.
+- -mkdir $(DS)
++ -mkdir -p $(DS)
+ cp $(S)/configure $(S)/*.in $(S)/bootstrap $(S)/README.build \
+ $(S)/NEWS $(S)/ChangeLog $(S)/global.mk $(S)/staden.profile $(DS)
+- -mkdir $(DS)/ac_stubs
++ -mkdir -p $(DS)/ac_stubs
+ cp $(S)/ac_stubs/*.m4 $(DS)/ac_stubs
+ #
+ # Recurse through sub-directories too
+@@ -143,22 +143,22 @@
+ chmod -R go-w $(DS)
+ #
+ # Windows compilation bits
+-# -mkdir $(S)/windows
++# -mkdir -p $(S)/windows
+ # cp -R windows/include $(S)
+-# -mkdir $(S)/mkdef
++# -mkdir -p $(S)/mkdef
+ # cp -R windows/mkdef/mkdef.* $(S)/mkdef
+-# -mkdir $(S)/run
++# -mkdir -p $(S)/run
+ # cp -R windows/run/run.* \
+ # windows/run/main.cpp\
+ # windows/run/notes.txt\
+ # windows/run/sprun.rc\
+ # windows/run/staden.ico\
+ # $(S)/run
+-# mkdir $(S)/windows/dumpenv
++# mkdir -p $(S)/windows/dumpenv
+ # cp -R windows/dumpenv/dumpenv.*\
+ # windows/dumpenv/main.cpp\
+ # $(S)/windows/dumpenv
+-# mkdir $(S)/windows/stashmsg
++# mkdir -p $(S)/windows/stashmsg
+ # cp -R windows/stashmsg/stashmsg.*\
+ # windows/stashmsg/icon1.ico\
+ # windows/stashmsg/messages.*\
diff --git a/sci-biology/staden/files/man-init-tar.patch b/sci-biology/staden/files/man-init-tar.patch
new file mode 100644
index 000000000..99e63db32
--- /dev/null
+++ b/sci-biology/staden/files/man-init-tar.patch
@@ -0,0 +1,14 @@
+--- doc/manual/manpages-t.texi.ori 2009-02-23 03:40:27.000000000 +0100
++++ doc/manual/manpages-t.texi 2009-02-23 03:40:30.000000000 +0100
+@@ -74,11 +74,6 @@
+ _include(hash_tar.1.texi)
+
+ @page
+-@node Man-init_tar
+-@chapter Init_tar
+-_include(init_tar.1.texi)
+-
+-@page
+ @node Man-makeSCF
+ @chapter MakeSCF
+ _include(makeSCF.1.texi)
diff --git a/sci-biology/staden/files/staden-src-1-7-0.patch2 b/sci-biology/staden/files/staden-src-1-7-0.patch2
new file mode 100644
index 000000000..03d05d5aa
--- /dev/null
+++ b/sci-biology/staden/files/staden-src-1-7-0.patch2
@@ -0,0 +1,270 @@
+diff -u -r staden-src-1-7-0.ori/course/texi/Makefile staden-src-1-7-0/course/texi/Makefile
+--- staden-src-1-7-0.ori/course/texi/Makefile 2006-07-05 13:05:50.000000000 +0200
++++ staden-src-1-7-0/course/texi/Makefile 2009-02-23 03:48:49.000000000 +0100
+@@ -55,7 +55,7 @@
+ #-----------------------------------------------------------------------------
+ # The main make targets.
+
+-all: unix windows
++all: windows
+
+ unix: course_unix.ps course_unix.pdf
+
+diff -u -r staden-src-1-7-0.ori/doc/manual/manpages-t.texi staden-src-1-7-0/doc/manual/manpages-t.texi
+--- staden-src-1-7-0.ori/doc/manual/manpages-t.texi 2006-07-04 18:17:37.000000000 +0200
++++ staden-src-1-7-0/doc/manual/manpages-t.texi 2009-02-23 03:40:30.000000000 +0100
+@@ -74,11 +74,6 @@
+ _include(hash_tar.1.texi)
+
+ @page
+-@node Man-init_tar
+-@chapter Init_tar
+-_include(init_tar.1.texi)
+-
+-@page
+ @node Man-makeSCF
+ @chapter MakeSCF
+ _include(makeSCF.1.texi)
+diff -u -r staden-src-1-7-0.ori/mklinks staden-src-1-7-0/mklinks
+--- staden-src-1-7-0.ori/mklinks 2006-06-28 17:51:59.000000000 +0200
++++ staden-src-1-7-0/mklinks 2009-02-23 02:13:44.000000000 +0100
+@@ -47,14 +47,6 @@
+ ln -s ../src/mutscan/$i-binaries/mutscan .
+ ln -s ../src/polyA_clip/$i-binaries/polyA_clip .
+ ln -s ../src/qclip/$i-binaries/qclip .
+- ln -s ../src/io_lib/progs/$i-binaries/convert_trace .
+- ln -s ../src/io_lib/progs/$i-binaries/extract_seq .
+- ln -s ../src/io_lib/progs/$i-binaries/index_tar .
+- ln -s ../src/io_lib/progs/$i-binaries/makeSCF .
+- ln -s ../src/io_lib/progs/$i-binaries/scf_dump .
+- ln -s ../src/io_lib/progs/$i-binaries/scf_info .
+- ln -s ../src/io_lib/progs/$i-binaries/scf_update .
+- ln -s ../src/io_lib/progs/$i-binaries/trace_dump .
+ ln -s ../src/screen_seq/$i-binaries/screen_seq .
+ ln -s ../src/tk_utils/$i-binaries/stash .
+ ln -s ../src/tracediff/$i-binaries/tracediff .
+diff -u -r staden-src-1-7-0.ori/src/Makefile staden-src-1-7-0/src/Makefile
+--- staden-src-1-7-0.ori/src/Makefile 2005-09-29 15:36:41.000000000 +0200
++++ staden-src-1-7-0/src/Makefile 2009-02-23 01:16:27.000000000 +0100
+@@ -12,7 +12,6 @@
+ include mk/global.mk
+
+ DIRS = Misc\
+- io_lib\
+ tk_utils\
+ text_utils\
+ seq_utils\
+@@ -108,11 +107,6 @@
+ # have been manually hacked/bug fixed.
+ distunix:
+ -mkdir $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libpng* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libtcl* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libtk* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libitcl* $(DIST)/lib/$(MACHINE)-binaries
+- -cp -R lib/$(MACHINE)-binaries/libitk* $(DIST)/lib/$(MACHINE)-binaries
+
+
+ distwindows:
+diff -u -r staden-src-1-7-0.ori/src/gap4/Makefile staden-src-1-7-0/src/gap4/Makefile
+--- staden-src-1-7-0.ori/src/gap4/Makefile 2005-08-25 12:20:49.000000000 +0200
++++ staden-src-1-7-0/src/gap4/Makefile 2009-02-23 03:33:34.000000000 +0100
+@@ -165,6 +165,9 @@
+ $(P3_LIB)
+
+ GAP4SH_LIBS=\
++ $(ZLIB_LIB) \
++ $(PNG_LIB) \
++ $(CURL_LIB) \
+ $(IOLIB_LIB) \
+ $(G_LIB) \
+ $(SEQUTILS_LIB) \
+diff -u -r staden-src-1-7-0.ori/src/mk/global.mk staden-src-1-7-0/src/mk/global.mk
+--- staden-src-1-7-0.ori/src/mk/global.mk 2006-06-08 15:15:58.000000000 +0200
++++ staden-src-1-7-0/src/mk/global.mk 2009-02-23 03:33:36.000000000 +0100
+@@ -128,10 +128,10 @@
+ XSRC =
+ TCLVERS = 8.4
+ TKVERS = 8.4
+-TCLSRC = $(SRCROOT)/tcl8.4.6/generic
+-TKSRC = $(SRCROOT)/tk8.4.6/generic
+-ITCLSRC = $(SRCROOT)/incrTcl-3.3cvs/itcl/generic
+-ITKSRC = $(SRCROOT)/incrTcl-3.3cvs/itk/generic
++TCLSRC = /usr/lib/tcl8.4/include/generic/
++TKSRC = /usr/lib/tk8.4/include/generic/
++ITCLSRC = /usr/lib/itcl3.3
++ITKSRC = /usr/lib/itk3.3
+ TTSRC =
+ ITCLVERS = 3.3
+ ITKVERS = 3.3
+@@ -187,6 +187,7 @@
+ MUT_LIB = $(MUT_LIB_S) $(LINK_LIBFLAG)mutlib$(LIB_EXT) $(MUT_LIB_E)
+ P3_LIB = $(P3_LIB_S) $(LINK_LIBFLAG)primer3$(LIB_EXT) $(P3_LIB_E)
+ PNG_LIB = $(PNG_LIB_S) $(LINK_LIBFLAG)png12$(LIB_EXT) $(PNG_LIB_E)
++CURL_LIB = $(CURL_LIB_S) $(LINK_LIBFLAG)curl$(LIB_EXT) $(CURL_LIB_E)
+
+
+ # Standard chunks to add to the compile line
+@@ -201,10 +202,10 @@
+ X_INC = $(XSRC:%=-I%)
+ XAW_INC = $(XSRC:%=-I%)
+ TT_INC = $(TTSRC:%=-I%)
+-IOLIB_INC = -I$(IOLIBSRC)/include
+-IOUTILS_INC = -I$(IOLIBSRC)/include
+-SCF_INC = -I$(IOLIBSRC)/include
+-EXP_INC = -I$(IOLIBSRC)/include
++IOLIB_INC = -I$(IOLIBSRC)
++IOUTILS_INC = -I$(IOLIBSRC)
++SCF_INC = -I$(IOLIBSRC)
++EXP_INC = -I$(IOLIBSRC)
+ G_INC = -I$(GSRC)
+ GAP4_INC = -I$(GAP4SRC)
+ NIP4_INC = -I$(NIP4SRC)
+@@ -290,7 +291,7 @@
+ GETSCFFIELD = $(SRCROOT)/get_scf_field
+ INDEXSEQLIBSSRC = $(SRCROOT)/indexseqlibs
+ INITEXPSRC = $(SRCROOT)/init_exp
+-IOLIBSRC = $(SRCROOT)/io_lib
++IOLIBSRC = /usr/include/io_lib
+ LOOKUPSRC = $(SRCROOT)/lookup
+ MAKESCFSRC = $(SRCROOT)/makeSCF
+ MISCSRC = $(SRCROOT)/Misc
+diff -u -r staden-src-1-7-0.ori/src/mk/linux.mk staden-src-1-7-0/src/mk/linux.mk
+--- staden-src-1-7-0.ori/src/mk/linux.mk 2005-08-25 12:22:20.000000000 +0200
++++ staden-src-1-7-0/src/mk/linux.mk 2009-02-23 03:35:37.000000000 +0100
+@@ -6,9 +6,10 @@
+ /* DEFINES += -DLITTLE_ENDIAN */
+
+ # Use g77 for compiling our fortran
+-F77 = g77
+-# Ewe:
+-F77_DEP = -lg2c
++F77 = gfortran
++# use for g77
++# F77_DEP = -lg2c
++F77_DEP = -lgfortran
+ LIBSF = $(F77_DEP)
+ # Jura
+ # F77_DEP = /usr/lib/gcc-lib/i386-glibc21-linux/egcs-2.91.66/libg2c.a
+@@ -31,8 +32,8 @@
+ XBIN = /usr/X11R6/lib
+ # For AMD64 based systems use XBIN=/usr/X11R6/lib64
+
+-#CLDFLAGS_E += -shared
+-#FLDFLAGS_E += -shared
++CLDFLAGS_E += -shared
++FLDFLAGS_E += -shared
+
+ # Dynamic linking
+ # For AMD64 based systems try -fPIC instead.
+@@ -41,7 +42,7 @@
+ # pic with g77 generates opcodes unknown by the 386 assembler. Odd
+ # It doesn't appear to be needed (but at a speed cost?).
+ # For AMD64 based systems try -fPIC instead.
+-#SHLIB_FFLAGS = -fpic
++SHLIB_FFLAGS = -fpic
+ SHLIB_LD = cc
+ SHLIB_LDFLAGS = -L$(L) $(SHLIB_STRIP) -shared -o
+ SHLIB_PREFIX = lib
+diff -u -r staden-src-1-7-0.ori/src/mk/root.mk staden-src-1-7-0/src/mk/root.mk
+--- staden-src-1-7-0.ori/src/mk/root.mk 2003-06-09 13:24:35.000000000 +0200
++++ staden-src-1-7-0/src/mk/root.mk 2009-02-23 02:07:43.000000000 +0100
+@@ -12,7 +12,6 @@
+ # gap/osp-bits
+ # gap
+ DIRS = Misc\
+- io_lib\
+ seq_utils\
+ tk_utils\
+ spin\
+@@ -55,13 +54,10 @@
+ # in io_lib from (eg) clean to cleanx.
+ #
+ clean:
+- cd io_lib; $(MAKE) $(FLAGS) cleanx
+- $(MAKE) $(FLAGS) JOB=clean
++ -echo blah
+
+ spotless:
+- cd io_lib; $(MAKE) $(FLAGS) spotlessx
+- $(MAKE) $(FLAGS) JOB=spotless
+- -rm lib/$(O)/so_locations
++ -ech blah
+
+ relink:
+ -rm lib/$(O)/so_locations
+diff -u -r staden-src-1-7-0.ori/src/mutlib/Makefile staden-src-1-7-0/src/mutlib/Makefile
+--- staden-src-1-7-0.ori/src/mutlib/Makefile 2004-10-28 11:15:56.000000000 +0200
++++ staden-src-1-7-0/src/mutlib/Makefile 2009-02-23 01:58:04.000000000 +0100
+@@ -63,8 +63,6 @@
+
+ MUT_DEP=\
+ $(SEQUTILS_LIB) \
+- $(TKUTILS_LIB) \
+- $(IOLIB_LIB) \
+ $(MISC_LIB) \
+ $(MATH_LIB)
+
+diff -u -r staden-src-1-7-0.ori/src/mutlib/staden.h staden-src-1-7-0/src/mutlib/staden.h
+--- staden-src-1-7-0.ori/src/mutlib/staden.h 2003-06-09 13:24:40.000000000 +0200
++++ staden-src-1-7-0/src/mutlib/staden.h 2009-02-23 02:21:50.000000000 +0100
+@@ -24,7 +24,7 @@
+
+ #include <Misc/misc.h>
+ #include <seq_utils/dna_utils.h>
+-#include <io_lib/include/Read.h>
++#include <io_lib/Read.h>
+
+
+ #ifdef __cplusplus
+diff -u -r staden-src-1-7-0.ori/src/mutscan/staden.h staden-src-1-7-0/src/mutscan/staden.h
+--- staden-src-1-7-0.ori/src/mutscan/staden.h 2003-06-09 13:25:30.000000000 +0200
++++ staden-src-1-7-0/src/mutscan/staden.h 2009-02-23 02:15:49.000000000 +0100
+@@ -22,7 +22,7 @@
+ #endif
+
+
+-#include <io_lib/include/Read.h>
++#include <io_lib/Read.h>
+ #include <licence/licence.h>
+
+
+diff -u -r staden-src-1-7-0.ori/src/tk_utils/Makefile staden-src-1-7-0/src/tk_utils/Makefile
+--- staden-src-1-7-0.ori/src/tk_utils/Makefile 2005-07-07 17:57:33.000000000 +0200
++++ staden-src-1-7-0/src/tk_utils/Makefile 2009-02-23 01:53:17.000000000 +0100
+@@ -72,12 +72,7 @@
+ @
+
+ TKU_LIBS = \
+- $(IOLIB_LIB) \
+- $(TK_LIB) \
+- $(TCL_LIB) \
+ $(MISC_LIB) \
+- $(PNG_LIB) \
+- $(ZLIB_LIB) \
+ $(SOCKET)
+
+ $(L)/$(SHLIB_PREFIX)$(LIBS)$(SHLIB_SUFFIX): $(OBJS) $(DEF_FILE)
+@@ -113,8 +108,8 @@
+ -ln -s ../licence/md52.c .
+ -ln -s ../licence/md52.h .
+ -ln -s ../licence/valid_seq.c .
+- -ln -s ../tcl8.4.6/unix/tclAppInit.c .
+- -ln -s ../tk8.4.6/winMain.c .
++ -ln -s /usr/lib/tcl8.4/tclAppInit.c .
++ # -ln -s ../tk8.4.6/winMain.c .
+ touch .links
+ $(MAKE) $(MFLAGS)
+
+diff -u -r staden-src-1-7-0.ori/src/tracediff/staden.h staden-src-1-7-0/src/tracediff/staden.h
+--- staden-src-1-7-0.ori/src/tracediff/staden.h 2003-06-09 13:25:23.000000000 +0200
++++ staden-src-1-7-0/src/tracediff/staden.h 2009-02-23 02:21:06.000000000 +0100
+@@ -22,7 +22,7 @@
+ #endif
+
+
+-#include <io_lib/include/Read.h>
++#include <io_lib/Read.h>
+ #include <licence/licence.h>
+
+
diff --git a/sci-biology/staden/files/system.mk.in.patch b/sci-biology/staden/files/system.mk.in.patch
new file mode 100644
index 000000000..365238035
--- /dev/null
+++ b/sci-biology/staden/files/system.mk.in.patch
@@ -0,0 +1,31 @@
+
+
+
+
+Index: system.mk.in
+===================================================================
+--- system.mk.in (revision 2261)
++++ system.mk.in (working copy)
+@@ -113,14 +113,14 @@
+
+ # Our libraries are I think exclusively used by us, hence we pick
+ # our own subdirectory.
+-prefix = ${DESTDIR}@prefix@
+-exec_prefix = ${DESTDIR}@exec_prefix@
+-INSTALLLIB = @libdir@/staden
+-INSTALLBIN = @bindir@
+-#INSTALLETC = @sysconfdir@/staden
+-INSTALLSHARE = @datadir@/staden
+-INSTALLDOC = @datadir@/doc
+-INSTALLMAN = @mandir@
++prefix = @prefix@
++exec_prefix = @exec_prefix@
++INSTALLLIB = ${DESTDIR}@libdir@/staden
++INSTALLBIN = ${DESTDIR}@bindir@
++#INSTALLETC = ${DESTDIR}@sysconfdir@/staden
++INSTALLSHARE = ${DESTDIR}@datadir@/staden
++INSTALLDOC = ${DESTDIR}@datadir@/doc
++INSTALLMAN = ${DESTDIR}@mandir@
+ INSTALLSCRIPTS = $(INSTALLSHARE)/scripts
+ INSTALLTCL = $(INSTALLSHARE)/tcl
+