cont. gene characterization

tool_setup.sh

@@ -82,4 +82,26 @@ pip install --user multiqc
 
 ## bedops
 tar xvf bedops_linux_x86_64-v2.4.20.tar.bz2
-mv bin bedops_linux_x86_64-v2.4.20
\ No newline at end of file
+mv bin bedops_linux_x86_64-v2.4.20
+
+
+## pfam (follow PfamScan/README and see http://pfam.xfam.org/help#tabview=tab12)
+
+cd /home/brandl/bin/PfamScan/pfam_data
+
+wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
+wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
+wget  ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz
+
+gunzip Pfam-A.hmm.dat.gz
+gunzip Pfam-A.hmm.gz
+gunzip active_site.dat.gz
+
+#which hmmpress
+export PATH=/projects/plantx/bin/hmmer-3.1b2-linux-intel-x86_64/binaries/:$PATH
+hmmpress Pfam-A.hmm
+
+
+wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz
+tar xvf PfamScan.tar.gz
+#cpan Moose ## suggested by does not seem to be required, see
\ No newline at end of file