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authorJeffrey Gardner <je_fro@gentoo.org>2007-10-02 04:35:49 +0000
committerJeffrey Gardner <je_fro@gentoo.org>2007-10-02 04:35:49 +0000
commitdab9f0b41c94b362dad8c86fb355f5cb9a7cf962 (patch)
tree9edde1f682a8388664b3c2e16a2284255529b3da /sci-biology/ncbi-tools/files
parentPoint to proper PATCHDIR. (diff)
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Testing new revision.
svn path=/; revision=84
Diffstat (limited to 'sci-biology/ncbi-tools/files')
-rw-r--r--sci-biology/ncbi-tools/files/21ncbi-r16
-rw-r--r--sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r18
-rw-r--r--sci-biology/ncbi-tools/files/digest-ncbi-tools-200708268
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch27
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch37
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-lop.patch15
-rw-r--r--sci-biology/ncbi-tools/files/ncbirc2
7 files changed, 103 insertions, 0 deletions
diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1
new file mode 100644
index 0000000..d4de68e
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/21ncbi-r1
@@ -0,0 +1,6 @@
+# Location of the formatdb data sets
+BLASTDB="/usr/share/ncbi/formatdb"
+# Location of the BLAST matrixes.
+BLASTMAT="/usr/share/ncbi/data"
+# Location of the ".ncbi.rc" file which sets the default path for shared data.
+NCBI=/etc/ncbi
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1
new file mode 100644
index 0000000..a80231e
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1
@@ -0,0 +1,8 @@
+MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
+RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
+SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
+MD5 8eca84753fd7a1d39bab256a4944f65e ncbi-tools-20061015.tar.gz 15772715
+RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 ncbi-tools-20061015.tar.gz 15772715
+SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de ncbi-tools-20061015.tar.gz 15772715
+RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
+SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
new file mode 100644
index 0000000..3c82f07
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
@@ -0,0 +1,8 @@
+MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
+RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
+SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
+MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175
+RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175
+SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175
+RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
+SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
new file mode 100644
index 0000000..1cd7976
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
@@ -0,0 +1,27 @@
+--- ncbi-20050605/make/makedis.csh 2005-05-13 05:42:12.000000000 +0200
++++ ncbi/make/makedis.csh 2005-09-20 22:02:38.000000000 +0200
+@@ -472,6 +472,24 @@
+
+ set net_stat = $status
+
++if ("$?NCBI_MT_OTHERLIBS" == "1") then
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ THREAD_OBJ=$NCBI_THREAD_OBJ \
++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++else
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++endif
++eval echo $CMD
++eval echo $CMD | sh
++
+ if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
+ echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
+ cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
new file mode 100644
index 0000000..cb7d1ad
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
@@ -0,0 +1,37 @@
+--- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200
++++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100
+@@ -485,6 +485,34 @@
+
+ set net_stat = $status
+
++if ( $net_stat == 0 ) then
++ # Compile additional tools, usually hidden
++ if ( ! $?EXTRA_VIB ) then
++ set EXTRA_VIB = ( asn2all )
++ endif
++
++ if ("$?NCBI_MT_OTHERLIBS" == "1") then
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ THREAD_OBJ=$NCBI_THREAD_OBJ \
++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
++ else
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
++ endif
++ eval echo $CMD
++ eval echo $CMD | sh
++
++ set net_stat = $status
++
++endif
++
+ if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
+ echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
+ cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
new file mode 100644
index 0000000..867b203
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
@@ -0,0 +1,15 @@
+--- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500
++++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500
+@@ -9,10 +9,10 @@
+ #it appears the flags above do not work anymore with newer libc,
+ #the new flags should work. Dima. 08/23/01
+ NCBI_AR=ar
+-NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
++NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+ NCBI_CFLAGS1 = -c
+ NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES
+-NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE
++NCBI_OPTFLAG = -O3 -D_LARGE_FILE
+ NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin
+ NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin
+ NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc
new file mode 100644
index 0000000..625dc6a
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbirc
@@ -0,0 +1,2 @@
+[NCBI]
+Data=/usr/share/ncbi/data