Fix perl shebangs to be portable and usable on Prefix. See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ --- a/easel/demotic/infernal_tab2gff.pl +++ b/easel/demotic/infernal_tab2gff.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic +#!/usr/bin/env perl # TAJ 6/23/08 last mod 7/10/08 # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format --- a/easel/demotic/test.pl +++ b/easel/demotic/test.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl use demotic_blast; --- a/easel/devkit/rmanprocess.pl +++ b/easel/devkit/rmanprocess.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # rmanprocess.pl # --- a/easel/miniapps/esl-afetch.itest.pl +++ b/easel/miniapps/esl-afetch.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Testing the esl-afetch miniapp # --- a/easel/miniapps/esl-alimanip.itest.pl +++ b/easel/miniapps/esl-alimanip.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-alimanip miniapp. # --- a/easel/miniapps/esl-alimap.itest.pl +++ b/easel/miniapps/esl-alimap.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-alimap miniapp. # --- a/easel/miniapps/esl-alimask.itest.pl +++ b/easel/miniapps/esl-alimask.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of esl-alimask miniapp. # --- a/easel/miniapps/esl-alimerge.itest.pl +++ b/easel/miniapps/esl-alimerge.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of esl-alimerge miniapp. # --- a/easel/miniapps/esl-alistat.itest.pl +++ b/easel/miniapps/esl-alistat.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-alistat miniapp. # --- a/easel/miniapps/esl-compalign.itest.pl +++ b/easel/miniapps/esl-compalign.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-compalign miniapp. # --- a/easel/miniapps/esl-construct.itest.pl +++ b/easel/miniapps/esl-construct.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-construct miniapp. # --- a/easel/miniapps/esl-mask.itest.pl +++ b/easel/miniapps/esl-mask.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of esl-mask miniapp. # --- a/easel/miniapps/esl-seqrange.itest.pl +++ b/easel/miniapps/esl-seqrange.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-seqrange miniapp. # --- a/easel/miniapps/esl-shuffle.itest.pl +++ b/easel/miniapps/esl-shuffle.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of esl-shuffle miniapp # --- a/easel/miniapps/esl-ssdraw.itest.pl +++ b/easel/miniapps/esl-ssdraw.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of the esl-ssdraw miniapp. # --- a/easel/testsuite/coverage_report.pl +++ b/easel/testsuite/coverage_report.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Measures testsuite coverage (as percentage of source lines), # using gcov. --- a/easel/testsuite/driver_report.pl +++ b/easel/testsuite/driver_report.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Make sure that all drivers compile. # (Eventually, we should also make sure they run! But that --- a/easel/testsuite/i1-degen-residues.pl +++ b/easel/testsuite/i1-degen-residues.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integration tests of reading all valid protein sequence residue characters. # --- a/easel/testsuite/i2-ncbi-indices.pl +++ b/easel/testsuite/i2-ncbi-indices.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Testing that we can read FASTA files, even if they have NCBI # formatted BLAST databases in the same directory. --- a/easel/testsuite/i3-blank-gf.pl +++ b/easel/testsuite/i3-blank-gf.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Bug #e5: blank text line following #=GF handled improperly. # --- a/easel/testsuite/valgrind_report.pl +++ b/easel/testsuite/valgrind_report.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Run the testsuite under Valgrind, to check for memory leakage. # --- a/profmark/pmark-master.pl +++ b/profmark/pmark-master.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl -w +#!/usr/bin/env perl # The top level script that runs a pmark benchmark. # --- a/profmark/rocplot.pl +++ b/profmark/rocplot.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl $nsearches = 2809; --- a/src/hmmpress.itest.pl +++ b/src/hmmpress.itest.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Integrated test of hmmpress # --- a/testsuite/i10-duplicate-names.pl +++ b/testsuite/i10-duplicate-names.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Check that we can deal with profiles and sequences that contain # duplicate names, both as queries and targets. --- a/testsuite/i11-hmmalign-mapali.pl +++ b/testsuite/i11-hmmalign-mapali.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Another test of the hmmalign --mapali option, after Elena reports # bug #h73 in bad interaction of checksum calculation and marking --- a/testsuite/i12-delete-corruption.pl +++ b/testsuite/i12-delete-corruption.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Bug #h77: hmmalign corrupts column preceding an all-delete column # --- a/testsuite/i13-msa-integrity.pl +++ b/testsuite/i13-msa-integrity.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Look for any problems in hmmalign that corrupt the input sequences. # --- a/testsuite/i14-hmmemit-consensus.pl +++ b/testsuite/i14-hmmemit-consensus.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Tests hmmemit -c and hmmemit -C consensus-generating options. # --- a/testsuite/i15-hmmconvert.pl +++ b/testsuite/i15-hmmconvert.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Bug #h80: hmmconvert can't read H2 Nucleic files # --- a/testsuite/i16-build-allins.pl +++ b/testsuite/i16-build-allins.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq # --- a/testsuite/i17-stdin.pl +++ b/testsuite/i17-stdin.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test that programs accept and reject argument of '-' (for reading # data from stdin, rather than from files) as they're supposed to. --- a/testsuite/i18-nhmmer-generic.pl +++ b/testsuite/i18-nhmmer-generic.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test of hmmbuild/nhmmer as used to build a DNA model, then query a # a database of long (1MB). --- a/testsuite/i19-hmmpgmd-ga.pl +++ b/testsuite/i19-hmmpgmd-ga.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test that hmmpgmd is correctly applying bit score thresholds; # in this case, the --cut_ga threshold, using an example that --- a/testsuite/i20-fmindex-core.pl +++ b/testsuite/i20-fmindex-core.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch # --- a/testsuite/i5-hmmbuild-naming.pl +++ b/testsuite/i5-hmmbuild-naming.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test that HMM naming in hmmbuild works as advertised. # Written to test for #h50. --- a/testsuite/i6-hmmalign-mapali.pl +++ b/testsuite/i6-hmmalign-mapali.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test the hmmalign --mapali option. # --- a/testsuite/i7-hmmbuild-fragments.pl +++ b/testsuite/i7-hmmbuild-fragments.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Test the ability of hmmbuild to deal with crappy alignments # of lots of sequence fragments. --- a/testsuite/i8-nonresidues.pl +++ b/testsuite/i8-nonresidues.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Regression test of handling a nonresidue '*' character. By design, # '*' residues score 0 in insert states and N,C,J; and -inf in match --- a/testsuite/i9-optional-annotation.pl +++ b/testsuite/i9-optional-annotation.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl +#!/usr/bin/env perl # Check that we can deal with HMMs with no optional annotation, in either # hmmscan or hmmsearch mode. --- a/testsuite/test-make.pl +++ b/testsuite/test-make.pl @@ -1,4 +1,4 @@ -#! /usr/bin/perl -w +#!/usr/bin/env perl # Usage: test-make.pl #