pfamserver stable port information

Package: pfamserver
Version: 7.6
Revision: 3
Source: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/%n-%v.tar.gz
Source2: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/Pfam_ls.gz
Source3: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/Pfam_fs.gz
Source4: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/Pfam-A.full.gz
Source5: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/Pfam-A.seed.gz
Source6: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/Pfam-B.gz
Source7: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/swisspfam.gz
Source8: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/pfamseq.gz
Source9: ftp://ftp.genetics.wustl.edu/pub/eddy/pfam/pfam-%v/domain.pnh.gz
Source-MD5: 803bcf3d8877fbbe0e816ae4d46e3d46
Source2-MD5: 1c8a0ea8e986d8c4a018a4735b1c8ecc
Source3-MD5: 99c493170665315d0c86b017660de46e
Source4-MD5: 477b285460a4270590dcfb1f56b707d8
Source5-MD5: 37ec6b75f94f33e9f9281d84f4663f2c
Source6-MD5: dc85b565459b09df810be1dde815b24f
Source7-MD5: dcd04286f547ed549ba5ae7b68a5a398
Source8-MD5: 3ca1d03d9810557d71c813d52bc90084
Source9-MD5: 96c8c398e1974752ba62b2bd728daf08
PatchFile: %n.patch
PatchFile-MD5: a0b9d320a3a378b3fab11775918bffb4
BuildDepends: fink (>= 0.24.12-1)
Depends: hmmer
CompileScript: <<
for file in fasta2gsi.pl makebrowse.pl makessi.pl pfam2desc.pl pfam2slx.pl pfamb2gsi.pl pfamconf.pl swisspfam2gsi.pl; do cp -p setup/$file setup/$file.dist; sed "s,/usr/local/bin/perl,/usr/bin/perl," < setup/$file.dist > setup/$file; chmod 755 setup/$file; done
for file in excuse.pl getalignment getdesc getdomainview gethmm getpfamb getspeciesdist getspeciesview getswisspfam nph-hmmsearch pnh-search textsearch; do cp -p cgi-bin/$file cgi-bin/$file.dist; sed "s,/usr/local/bin/perl,/usr/bin/perl," < cgi-bin/$file.dist > cgi-bin/$file; chmod 755 cgi-bin/$file; done

for file in Pfam_ls Pfam_fs Pfam-A.full Pfam-A.seed Pfam-B swisspfam pfamseq domain.pnh; do ln -s ../../$file.gz pfamdist; done
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do cp -p %p/bin/$file bin; done
for file in afetch alistat seqstat sfetch shuffle sindex sreformat; do cp -p %p/bin/$file bin; done
mkdir Desc Full Seed Otherdata docs/browse
echo Building the description file directory, Desc/...
(cd Desc; gunzip -c ../pfamdist/Pfam-A.full.gz | ../setup/pfam2desc.pl)
sort -f -o INDEX INDEX
mv INDEX conf/
echo Building the full alignments directory, Full/...
(cd Full; gunzip -c ../pfamdist/Pfam-A.full.gz | ../setup/pfam2slx.pl)
echo Building the seed alignments directory, Seed/...
(cd Seed; gunzip -c ../pfamdist/Pfam-A.seed.gz | ../setup/pfam2slx.pl)
echo Building binary HMM databases in Otherdata/...
(cd pfamdist; gunzip -c Pfam_fs.gz > Pfam_fs)
(cd pfamdist; gunzip -c Pfam_ls.gz > Pfam_ls)
(cd pfamdist; ../bin/hmmconvert -b Pfam_fs ../Otherdata/Pfam_fs%v)
(cd pfamdist; ../bin/hmmconvert -b Pfam_ls ../Otherdata/Pfam_ls%v)
(cd Otherdata; ../bin/hmmindex Pfam_fs%v)
(cd Otherdata; ../bin/hmmindex Pfam_ls%v)
gunzip -c pfamdist/Pfam-B.gz > Otherdata/Pfam-B
gunzip -c pfamdist/swisspfam.gz > Otherdata/swisspfam
gunzip -c pfamdist/pfamseq.gz > Otherdata/pfamseq
gunzip -c pfamdist/domain.pnh.gz > Otherdata/domain.pnh
(cd Otherdata; ../bin/sindex pfamseq)
(cd Otherdata; ../setup/pfamb2gsi.pl Pfam-B)
(cd Otherdata; ../setup/swisspfam2gsi.pl swisspfam)
(cd conf; host1=`hostname -s`; host2=`hostname | sed "s/^$host1\.//"`; cp -p pfamconf.pl pfamconf.pl.dist; sed "s,/home/www/pfam/pfamserver-%v,%p/share/%n-%v,g" < pfamconf.pl.dist | sed "s,yoyodyne\.com,$host2,g" | sed "s,Yoyodyne,$host2,g" > pfamconf.pl; chmod 755 pfamconf.pl)
(cd conf; sed "s,%p/share/%n-%v,..,g" < pfamconf.pl > pfamconf.pl.tmp)
(cd setup; ln -s ../conf/pfamconf.pl.tmp)
(cd setup; sed "s/pfamconf\.pl/pfamconf.pl.tmp/g" < makebrowse.pl | perl)
(cd setup; sed "s/pfamconf\.pl/pfamconf.pl.tmp/g" < makessi.pl | perl)
rm setup/pfamconf.pl.tmp conf/pfamconf.pl.tmp
echo Phew. Done!
<<
InstallScript: <<
install -d -m 755 %i/share/%n-%v
for dir in Desc Full Otherdata Seed bin cgi-bin conf docs setup; do cp -rp $dir %i/share/%n-%v/$dir; done
for dir in tmp logs docs/images/tmp; do install -d -m 755 %i/share/%n-%v/$dir; done
ln -s %n-%v %i/share/%n
<<
PostInstScript: <<
chown -R www:www %p/share/%n-%v
echo "****************************************"
echo "For %n to work, you must edit /etc/httpd/httpd.conf."
echo "Uncomment the \"AddHandler cgi-script .cgi\" line,"
echo "the \"AddType text/html .shtml\" line, and"
echo "the \"AddHandler server-parsed .shtml\" line."
echo "Add the following two sections:"
echo ""
echo ""
echo " Options FollowSymLinks ExecCGI Includes"
echo " AllowOverride None"
echo " Order allow,deny"
echo " Allow from all"
echo ""
echo ""
echo ""
echo " ServerName pfam.your.domain"
echo " DocumentRoot %p/share/%n/docs"
echo " ScriptAlias /cgi-bin/ %p/share/%n/cgi-bin/"
echo ""
echo ""
echo "Also, you will have to add the host pfam.your.domain to NetInfo."
echo "You can do this through the NetInfo GUI or the shell. For example,"
echo "the following three lines will assign the name to your local host:"
echo "sudo niload hosts / < echo "127.0.0.1 pfam.your.domain"
echo "EOF"
echo "where \"your.domain\" is the name of your domain."
echo "Then restart apache:"
echo "sudo apachectl restart"
echo "****************************************"
echo "To demonstrate %n, point your browser to:"
echo "http://pfam.your.domain/"
echo "****************************************"
echo "For more information, see:"
echo "http://pfam.wustl.edu/"
echo "http://hmmer.wustl.edu/"
<<
DocFiles: 00README COPYRIGHT INSTALL LICENSE Makefile
License: Public Domain
Description: WWW Pfam server
DescDetail: <<
Pfam is a large collection of multiple sequence alignments and hidden
Markov models covering many common protein domains.
<<
DescUsage: <<
****************************************
For %n to work, you must edit /etc/httpd/httpd.conf.
Uncomment the \"AddHandler cgi-script .cgi\" line,
the \"AddType text/html .shtml\" line, and
the \"AddHandler server-parsed .shtml\" line.
Add the following two sections:


Options FollowSymLinks ExecCGI Includes
AllowOverride None
Order allow,deny
Allow from all



ServerName pfam.your.domain
ScriptAlias /cgi-bin/ %p/share/%n/cgi-bin/
DocumentRoot %p/share/%n/docs


Also, you will have to add the host pfam.your.domain to NetInfo.
You can do this through the NetInfo GUI or the shell. For example,
the following three lines will assign the name to your local host:
sudo niload hosts / < 127.0.0.1 pfam.your.domain
EOF
where \"your.domain\" is the name of your domain.
Then restart apache:
sudo apachectl restart
****************************************
To demonstrate %n, point your browser to:
http://pfam.your.domain/
****************************************
For more information, see:"
http://pfam.wustl.edu/
http://hmmer.wustl.edu/
<<
Maintainer: Richard Graul
Homepage: http://pfam.wustl.edu/

pfamserver stable port .patch

--- pfamserver/conf/pfamconf.pl Thu Sep 19 12:55:41 2002
+++ pfamserver/conf/pfamconf.pl Thu Apr 17 20:53:15 2003
@@ -19,12 +19,12 @@
# The --cpu option lets you limit the number of CPUs that will be devoted
# to Pfam HMM searches.
#
-$WULFPACKDATA = "/data/wulfpack"; # Install directory on compute cluster
+#$WULFPACKDATA = "/data/wulfpack"; # Install directory on compute cluster
# machines
-$SEARCHOPTS = "--pvm"; # Run searches using a PVM cluster.
+#$SEARCHOPTS = "--pvm"; # Run searches using a PVM cluster.

-#$WULFPACKDATA = ""; # Alternatively: no compute cluster...
-#$SEARCHOPTS = "--cpu 3"; # limit to 3 CPUs (e.g. on a 4-processor
+$WULFPACKDATA = ""; # Alternatively: no compute cluster...
+$SEARCHOPTS = "--cpu 1"; # limit to 1 CPUs (e.g. on a 2-processor
# machine)
# The next group controls options for the pfamserver.
# Set to '1' to enable, '0' to disable

pfamserver _unstable_ port .patch