calculate
/
gentoo-overlay
6
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Branches Tags
${ item.name }
Create tag ${ searchTerm }
Create branch ${ searchTerm }
from '1958'
${ noResults }
gentoo-overlay/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-sh...

332 lines
8.4 KiB
Raw Permalink Blame History

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 <rman LaTeX2e output>
#
--- 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 <tag> 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 <builddir> <srcdir> <tmppfx>
#
Reference in new issue View Git Blame Copy Permalink