Author: Michael R. Crusoe <crusoe@debian.org>
Description: adjust for installed use
Forwarded: non-needed
--- fasta3.orig/scripts/ann_exons_all.pl
+++ fasta3/scripts/ann_exons_all.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_exons_ens.pl
+++ fasta3/scripts/ann_exons_ens.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_exons_ncbi.pl
+++ fasta3/scripts/ann_exons_ncbi.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # ann_exons_ncbi.pl gets an annotation file from fasta36 -V with a line of the form:
 
--- fasta3.orig/scripts/ann_exons_up_sql.pl
+++ fasta3/scripts/ann_exons_up_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_exons_up_sql_www.pl
+++ fasta3/scripts/ann_exons_up_sql_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_exons_up_www.pl
+++ fasta3/scripts/ann_exons_up_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_feats2ipr.pl
+++ fasta3/scripts/ann_feats2ipr.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_feats2ipr_e.pl
+++ fasta3/scripts/ann_feats2ipr_e.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_feats_up_sql.pl
+++ fasta3/scripts/ann_feats_up_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_feats_up_www2.pl
+++ fasta3/scripts/ann_feats_up_www2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_ipr_www.pl
+++ fasta3/scripts/ann_ipr_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_pdb_cath.pl
+++ fasta3/scripts/ann_pdb_cath.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_pdb_vast.pl
+++ fasta3/scripts/ann_pdb_vast.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014, 2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_pfam30_tmptbl.pl
+++ fasta3/scripts/ann_pfam30_tmptbl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_pfam_sql.pl
+++ fasta3/scripts/ann_pfam_sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_pfam_www.pl
+++ fasta3/scripts/ann_pfam_www.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014, 2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/ann_upfeats_pfam_www_e.pl
+++ fasta3/scripts/ann_upfeats_pfam_www_e.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/annot_blast_btop2.pl
+++ fasta3/scripts/annot_blast_btop2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2017,2018 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/annot_blast_btop3.py
+++ fasta3/scripts/annot_blast_btop3.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 ################################################################
 # copyright (c) 2017,2018 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/annot_blast_btop4.py
+++ fasta3/scripts/annot_blast_btop4.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 ################################################################
 # copyright (c) 2017,2018 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/blastp_annot_cmd.sh
+++ fasta3/scripts/blastp_annot_cmd.sh
@@ -82,19 +82,19 @@
 
 # annot_cmd="annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann"
 # echo "# $annot_cmd"
-annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
+/usr/share/fasta3/scripts/annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
 
 if [[ $DO_HTML == 1 ]]; then
     ## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
     $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
     ## echo "# merge_blast_btab.pl --plot_url=plot_domain6t.cgi --have_qslen --dom_info --btab $blt_out $bl0_out"
-    merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blt_ann $bl0_out
+    /usr/share/fasta3/scripts/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blt_ann $bl0_out
 
 else
     $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 > $bl0_out
     merge_cmd="merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out"
     # echo "# $merge_cmd"
-    merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out
+    /usr/share/fasta3/scripts/merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out
 fi
 
 # $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2  > $blm_out
--- fasta3.orig/scripts/blastp_cmd.sh
+++ fasta3/scripts/blastp_cmd.sh
@@ -22,7 +22,7 @@
 # echo "OUTFILE = ${OUTNAME}"
 
 #export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
-export BLAST_PATH="/seqprg/bin"
+export BLAST_PATH="/usr/bin"
 
 $BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
 $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
--- fasta3.orig/scripts/exp_up_ensg.pl
+++ fasta3/scripts/exp_up_ensg.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/expand_links.pl
+++ fasta3/scripts/expand_links.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/expand_refseq_isoforms.pl
+++ fasta3/scripts/expand_refseq_isoforms.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/expand_uniref50.pl
+++ fasta3/scripts/expand_uniref50.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/expand_up_isoforms.pl
+++ fasta3/scripts/expand_up_isoforms.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/fasta_annot_cmd.sh
+++ fasta3/scripts/fasta_annot_cmd.sh
@@ -54,7 +54,7 @@
 blt_out="$OUTNAME.fa_tab"
 blr_out="$OUTNAME.fa_tab_rn"
 
-export BLAST_PATH="/seqprg/bin"
+export BLAST_PATH="/usr/bin"
 # BLAST_PATH="../bin"
 
 cmd="$cmd -mF8CBL=$blt_out $QUERY $DATABASE"
@@ -73,7 +73,7 @@
 # run the program
 $BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
 
-$BLAST_PATH/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
+/usr/share/fasta3/scripts/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
 
 if [ ! -s $blr_out ]; then
     # echo "# " `ls -l $blt_out $blr_out`
@@ -81,4 +81,4 @@
     # echo "# " `ls -l $blt_out $blr_out`
 fi
 
-$BLAST_PATH/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
+/usr/share/fasta3/scripts/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
--- fasta3.orig/scripts/get_genome_seq.py
+++ fasta3/scripts/get_genome_seq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 ################
 ## get_hg38_bed.py parses an HG38 coordinate into a pseudo-bed entry,
--- fasta3.orig/scripts/get_protein.py
+++ fasta3/scripts/get_protein.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 ## get_protein_www.py -- 
 ## get a protein sequence from the Uniprot or NCBI/Refseq web sites using the accession
--- fasta3.orig/scripts/get_protein_sql.py
+++ fasta3/scripts/get_protein_sql.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 ## get_protein_sql.py -- 
 ## get a protein sequence from a local Uniprot or NCBI/Refseq mySQL database using the accession
--- fasta3.orig/scripts/get_protein_sql_www.py
+++ fasta3/scripts/get_protein_sql_www.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 ## get_protein.py -- 
 ## get a protein sequence from Uniprot or NCBI/Refseq using the accession
--- fasta3.orig/scripts/get_refseq.py
+++ fasta3/scripts/get_refseq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 import sys
 import re
--- fasta3.orig/scripts/get_uniprot.py
+++ fasta3/scripts/get_uniprot.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 import sys
 import re
--- fasta3.orig/scripts/get_up_prot_iso_sql.py
+++ fasta3/scripts/get_up_prot_iso_sql.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 import sys
 import re
--- fasta3.orig/scripts/lav2plt.pl
+++ fasta3/scripts/lav2plt.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # lav2plt.pl - produce plotfrom lav output */
 
--- fasta3.orig/scripts/lavplt_ps.pl
+++ fasta3/scripts/lavplt_ps.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 ################################################################
 # copyright (c) 2012, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/lavplt_svg.pl
+++ fasta3/scripts/lavplt_svg.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 ################################################################
 # copyright (c) 2012, 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/links2sql.pl
+++ fasta3/scripts/links2sql.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/m8_btop_msa.pl
+++ fasta3/scripts/m8_btop_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/m9B_btop_msa.pl
+++ fasta3/scripts/m9B_btop_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/map_exon_coords.py
+++ fasta3/scripts/map_exon_coords.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 # 
 # given a -m8CB file with exon annotations for the query and subject,
 # provide a function that maps subject coordinates to query, or vice versa
--- fasta3.orig/scripts/merge_blast_btab.pl
+++ fasta3/scripts/merge_blast_btab.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2018 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/merge_fasta_btab.pl
+++ fasta3/scripts/merge_fasta_btab.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2018 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/relabel_domains.py
+++ fasta3/scripts/relabel_domains.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 # Given a blast_tabular file with search results from one or more
 # protein queries, modify the domain color numbers (e.g. ~1, ~2) so
--- fasta3.orig/scripts/rename_exons.py
+++ fasta3/scripts/rename_exons.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 # 
 # given a -m8CB file with exon annotations for the query and subject,
 # adjust the subject exon names to match the query exon names
--- fasta3.orig/scripts/summ_domain_ident.pl
+++ fasta3/scripts/summ_domain_ident.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014 by William R. Pearson and The Rector &
--- fasta3.orig/scripts/test_py.sh
+++ fasta3/scripts/test_py.sh
@@ -5,39 +5,39 @@
 ## test python scripts
 ##
 
-echo 'get_genome_seq.py'
-get_genome_seq.py chr1:109687874-109687909
+# echo 'get_genome_seq.py'
+# /usr/share/fasta3/scripts/get_genome_seq.py chr1:109687874-109687909
 
 echo 'get_protein.py'
-get_protein.py 'sp|P09488|GSTM1_HUMAN'
-get_protein.py 'P09488'
-get_protein.py 'NP_000552'
+/usr/share/fasta3/scripts/get_protein.py 'sp|P09488|GSTM1_HUMAN'
+/usr/share/fasta3/scripts/get_protein.py 'P09488'
+/usr/share/fasta3/scripts/get_protein.py 'NP_000552'
 
 echo 'get_refseq.py'
-get_refseq.py NP_000552
-get_refseq.py NP_0000552
+/usr/share/fasta3/scripts/get_refseq.py NP_000552
+/usr/share/fasta3/scripts/get_refseq.py NP_0000552
 
 echo 'get_uniprot.py'
-get_uniprot.py P09488
-get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
+/usr/share/fasta3/scripts/get_uniprot.py P09488
+/usr/share/fasta3/scripts/get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
 
 echo '################################################################'
 echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
 # (a) produce an appropriate alignment file
-fasta36 -q -m 8CBL -V \!ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!ann_exons_up_sql.pl+--gen_coord+--exon_label \!get_protein.py+P30711 \!get_protein.py+P20135 > hum_chk_map_test.m8CBL
+fasta36 -q -m 8CBL -V \!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/scripts/get_protein.py+P30711 \!/usr/share/fasta3/scripts/get_protein.py+P20135 > hum_chk_map_test.m8CBL
 # (b) expand chromosome locations on subject and query exons to both genomes
-map_exon_coords.py  hum_chk_map_test.m8CBL
+/usr/share/fasta3/scripts/map_exon_coords.py  hum_chk_map_test.m8CBL
 
 echo 'rename_exons.py -- look for exon_X in output'
-rename_exons.py hum_chk_map_test.m8CBL   # produces a renamed exon_x
-
-echo '################################################################'
-echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
-# (a) from FASTA -m8CBl -- no raw score
-echo '.fa_tab no raw score'
-annot_blast_btop4.py --no_raw_score --have_qslen --query ../seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
-
-## .bl_tab uses --ann_script because of multiple HSPs
-echo '.bl_tab yes raw score'
-annot_blast_btop4.py --raw_score --have_qslen --query ../seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
+/usr/share/fasta3/scripts/rename_exons.py hum_chk_map_test.m8CBL   # produces a renamed exon_x
 
+# echo '################################################################'
+# echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
+# # (a) from FASTA -m8CBl -- no raw score
+# echo '.fa_tab no raw score'
+# /usr/share/fasta3/scripts/annot_blast_btop4.py --no_raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
+# 
+# ## .bl_tab uses --ann_script because of multiple HSPs
+# echo '.bl_tab yes raw score'
+# /usr/share/fasta3/scripts/annot_blast_btop4.py --raw_score --have_qslen --query /usr/share/doc/fasta3/examples/seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
+# 
--- fasta3.orig/scripts/test_ann_scripts.sh
+++ fasta3/scripts/test_ann_scripts.sh
@@ -9,22 +9,22 @@
 # SP:GSTM1_HUMAN -- ebi searches without accession
 ##
 
-if [ ! $1=='' ]; then
+if [ ! "$1" = '' ]; then
    script_file=$1
 else
-    script_file=ann_script_list
+   script_file=/usr/share/fasta3/scripts/ann_script_list
 fi
 
-if [ ! $1=='' ]; then
+if [ ! "$1" = '' ]; then
    ex_file=$1
 else
-    ex_file=acc_examples
+   ex_file=/usr/share/fasta3/scripts/acc_examples
 fi
 
-for script in `cat $script_file `; do
-  for acc_type in `cat $ex_file`; do
-      echo $script ${acc_type}
-      $script ${acc_type}
-  done
-  echo '***DONE***'  $script `date`
-done
+while read -r script ; do
+  while read -r acc_type ; do
+      echo "${script}" "${acc_type}"
+      "${script}" "${acc_type}"
+  done < ${ex_file}
+  echo '***DONE***'  "$script" "$(date)"
+done < ${script_file}
--- fasta3.orig/scripts/ann_script_list
+++ fasta3/scripts/ann_script_list
@@ -1,9 +1,5 @@
-ann_exons_up_sql.pl
-ann_exons_up_www.pl
-ann_feats2ipr.pl
-ann_feats_up_sql.pl
-ann_feats_up_www2.pl
-ann_ipr_www.pl
-ann_pfam30.pl
-ann_pfam_www.pl
-ann_upfeats_pfam_www_e.pl
+/usr/share/fasta3/scripts/ann_exons_up_www.pl
+/usr/share/fasta3/scripts/ann_feats_up_sql.pl
+/usr/share/fasta3/scripts/ann_feats_up_www2.pl
+/usr/share/fasta3/scripts/ann_ipr_www.pl
+/usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl
--- fasta3.orig/psisearch2/clustal2fasta.pl
+++ fasta3/psisearch2/clustal2fasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/psisearch2/clustal2fasta.py
+++ fasta3/psisearch2/clustal2fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/psisearch2/m89_btop_msa2.pl
+++ fasta3/psisearch2/m89_btop_msa2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2014,2015 by William R. Pearson and The Rector &
--- fasta3.orig/psisearch2/psisearch2_msa.pl
+++ fasta3/psisearch2/psisearch2_msa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ################################################################
 # copyright (c) 2016,2020 by William R. Pearson and The Rector &
@@ -54,7 +54,7 @@
 # (3) NCBI blast+ programs: psiblast/makeblastdb
 # (4) NCBI datatool (required only for ssearch36 PSSMs)
 
-my $pgm_bin = "/seqprg/bin";
+my $pgm_bin = "/usr/bin";
 
 my $pgm_data = "/seqprg/data";
 my $ssearch_bin = "$pgm_bin/ssearch36";
--- fasta3.orig/psisearch2/psisearch2_msa.py
+++ fasta3/psisearch2/psisearch2_msa.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 ################################################################
 # copyright (c) 2016 by William R. Pearson and The Rector &
@@ -45,7 +45,7 @@
 # (3) NCBI blast+ programs: psiblast/makeblastdb
 # (4) NCBI datatool (required only for ssearch36 PSSMs)
 
-pgm_bin = "/seqprg/bin"
+pgm_bin = "/usr/bin"
 pgm_data = "/seqprg/data"
 ssearch_bin = pgm_bin+"/ssearch36"
 psiblast_bin = pgm_bin+"/psiblast"
@@ -54,9 +54,9 @@
 align2msa_lib = "m89_btop_msa2.pl"
 clustal2fasta = "clustal2fasta.py"
 
-annot_cmds = {'rpd3': '"!../scripts/ann_pfam28.pl --pfacc --db RPD3 --vdoms --split_over"',
-              'rpd3nv':'"!../scripts/ann_pfam28.pl --pfacc --db RPD3 --split_over"',
-              'pfam':'"!../scripts/ann_pfam30.pl --pfacc --vdoms --split_over"'}
+annot_cmds = {'rpd3': '"!/usr/share/fasta3/scripts/ann_pfam28.pl --pfacc --db RPD3 --vdoms --split_over"',
+              'rpd3nv':'"!/usr/share/fasta3/scripts/ann_pfam28.pl --pfacc --db RPD3 --split_over"',
+              'pfam':'"!/usr/share/fasta3/scripts/ann_pfam30.pl --pfacc --vdoms --split_over"'}
 
 num_iter = 5
 srch_pgm = 'ssearch'
--- fasta3.orig/psisearch2/psisearch2_msa_iter.sh
+++ fasta3/psisearch2/psisearch2_msa_iter.sh
@@ -7,8 +7,8 @@
 #
 
 
-PS_BIN=~/Devel/fa36_v3.8/psisearch2
-Q_DIR="../seq"
+PS_BIN=/usr/share/fasta3/psisearch2
+Q_DIR=/usr/share/doc/fasta3/examples/
 FA_DB=/slib2/fa_dbs/qfo78.lseg
 BL_DB=/slib2/bl_dbs/qfo78
 DB=$FA_DB
--- fasta3.orig/psisearch2/psisearch2_msa_iter_bl.sh
+++ fasta3/psisearch2/psisearch2_msa_iter_bl.sh
@@ -6,7 +6,7 @@
 # psisearch2_msa.pl --pgm psiblast --query query.aa --num_iter 5 --db /slib2/bl_dbs/qfo78
 #
 
-PS_BIN=~/Devel/fa36_v3.8/psisearch2
+PS_BIN=/usr/share/fasta3/psisearch2
 q_file=$1
 
 db=/slib2/bl_dbs/pir1
