Update of /cvsroot/fink/dists/10.2/unstable/main/finkinfo/sci
In directory usw-pr-cvs1:/tmp/cvs-serv25782
Added Files:
hmmer-2.2g-2.info hmmer-2.2g-2.patch
Log Message:
new package from tracker
--- NEW FILE: hmmer-2.2g-2.info ---
Package: hmmer
Version: 2.2g
Revision: 2
Source: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/%v/hmmer-%v.tar.gz
Source-MD5: d7def2007a0aaf2eafb9a96a07986b8c
Source2: http://pfam.wustl.edu/cgi-bin/gethmm\?name=7tm_1\&type=fs
Source2Rename: 7tm_1
Source3: http://us.expasy.org/cgi-bin/get-sprot-fasta\?P08908
Source3Rename: P08908.fasta
Patch: %f.patch
ConfigureParams: --bindir=%i/bin --mandir=%i/share/man
CompileScript: <<
./configure %c
make
make check
chmod a+r documentation/man/*
chmod a+r squid/Man/*
<<
InstallScript: <<
install -d -m 755 %i/bin
install -d -m 755 %i/share/man/man1
mv INSTALL INSTALL.sav
make install prefix=%i
mv INSTALL.sav INSTALL
install -d -m 755 %i/include/%n-%v
install -c -p -m 644 version.h src/*.h %i/include/%n-%v
ln -s %n-%v %i/include/%n
install -d -m 755 %i/lib
install -c -p -m 644 src/libhmmer.a %i/lib/libhmmer-%v.a
ln -s libhmmer-%v.a %i/lib/libhmmer.a
install -d -m 755 %i/share/%n/demo
install -c -p -m 644 ../7tm_1 %i/share/%n/demo
install -c -p -m 644 ../P08908.fasta %i/share/%n/demo
echo "#!/bin/sh" > %i/share/%n/demo/hmmsearch.sh
echo "hmmsearch %p/share/%n/demo/7tm_1 %p/share/%n/demo/P08908.fasta" >>
%i/share/%n/demo/hmmsearch.sh
chmod 755 %i/share/%n/demo/hmmsearch.sh
<<
PostInstScript: <<
echo "****************************************"
echo "For %n to work, you must set an environment variable"
echo "1) add the following to your ~/.profile", or
echo "# path to HMM libraries"
echo "HMMERDB=/data/hmmerdb ;export HMMERDB"
echo "2) add the following to your ~/.cshrc or ~/.tcshrc"
echo "# path to HMM libraries"
echo "setenv HMMERDB /data/hmmerdb"
echo "****************************************"
echo "To demonstrate %n, run:"
echo "%p/share/%n/demo/hmmsearch.sh"
echo "****************************************"
echo "You may manually download any HMM libraries to /data/hmmerdb from:"
echo "ftp://ftp.genetics.wustl.edu/pub/eddy/Pfam/";
echo "For more information, see:"
echo "http://hmmer.wustl.edu/";
echo "http://pfam.wustl.edu/";
<<
DocFiles: 00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
License: GPL
Description: profile hidden Markov models for biological sequence analysis
DescDetail: <<
HMMER - profile hidden Markov models for biological sequence analysis
Version 2.2 (August 2001)
Copyright (C) 1992-2001 Washington University School of Medicine
------------------------------------------------------------------
o About this software...
HMMER is an implementation of profile HMM methods for
sensitive database searches using multiple sequence alignments as queries.
Basically, you give HMMER a multiple sequence alignment as input;
it builds a statistical model called a "hidden Markov model"
which you can then use as a query into a sequence database
to find (and/or align) additional homologues of the sequence family.
<<
DescUsage: <<
For %n to work, you must set an environment variable
1) add the following to your ~/.profile, or
# path to HMM libraries
HMMERDB=/data/hmmerdb ;export HMMERDB
2) add the following to your ~/.cshrc or ~/.tcshrc
# path to HMM libraries
setenv HMMERDB /data/hmmerdb
To demonstrate %n, run:
%p/share/%n/demo/hmmsearch.sh
You may manually download any HMM libraries to /data/hmmerdb from:
ftp://ftp.genetics.wustl.edu/pub/eddy/Pfam/
For more information, see:
http://hmmer.wustl.edu/
http://pfam.wustl.edu/
<<
Maintainer: Richard Graul <[EMAIL PROTECTED]>
Homepage: http://hmmer.wustl.edu/
--- NEW FILE: hmmer-2.2g-2.patch ---
--- hmmer-2.2g-0/config.guess Sun Aug 5 16:55:36 2001
+++ hmmer-2.2g-1/config.guess Thu Mar 28 14:27:20 2002
@@ -801,6 +801,15 @@
echo mips-unknown-sysv${UNAME_RELEASE}
fi
exit 0 ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit 0 ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit 0 ;;
+ *:Darwin:*:* | *:"Mac OS":*:*)
+ echo `uname -p`-apple-darwin${UNAME_RELEASE}
+ exit 0 ;;
BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
echo powerpc-be-beos
exit 0 ;;
--- hmmer-2.2g-0/config.sub Sun Aug 5 16:55:45 2001
+++ hmmer-2.2g-1/config.sub Thu Mar 28 14:28:51 2002
@@ -714,7 +714,7 @@
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
| -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -mingw32* | -linux-gnu* | -uxpv* | -beos*)
+ | -mingw32* | -linux-gnu* | -uxpv* | -openstep* | -rhapsody* | -darwin*
+| -beos*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-linux*)
--- hmmer-2.2g-0/Makefile.in Aug 5 16:55:36 2001
+++ hmmer-2.2g-0/Makefile.in Jun 29 12:42:33 2002
@@ -146,7 +146,7 @@
for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
cp binaries/$$file $(BINDIR)/;\
done
- for file in hmmer $(PROGS) $(SQUIDPROGS); do\
+ for file in hmmer $(PROGS); do\
$(INSTMAN) documentation/man/$$file.man
$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
done
for file in $(SQUIDPROGS); do\
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