reinit the tree, so we can have metadata

4 files changed, 550 insertions, 0 deletions

diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
new file mode 100644
index 000000000000..110c61f11821
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
@@ -0,0 +1,22 @@
+Make the build system respect DESTDIR, in order to allow staged builds.
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -109,13 +109,13 @@
+ #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
+ #          Creates these directories if they don't exist.
+ install: 
+-	mkdir -p ${BINDIR}
+-	-mkdir -p ${MANDIR}/man${MANSUFFIX}
++	mkdir -p ${DESTDIR}${BINDIR}
++	-mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX}
+ 	for file in $(PROGS) $(PVMPROGS); do\
+-	   cp src/$$file $(BINDIR)/;\
++	   cp src/$$file ${DESTDIR}$(BINDIR)/;\
+ 	done
+ 	-for file in hmmer $(PROGS); do\
+-	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	   $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ 	done
+ 
+ # uninstall: Reverses the steps of "make install".
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
new file mode 100644
index 000000000000..783d0530aa7a
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
@@ -0,0 +1,108 @@
+* Fix ancient perl 4 modules that are long gone.
+* 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/squid/Testsuite/bug-1-sfetch-paths
++++ b/squid/Testsuite/bug-1-sfetch-paths
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test for bug #1: sfetch/SSI path bug.
+ # sfetch can't follow paths out of current directory if it's using
+--- a/squid/Testsuite/x-base-afetch
++++ b/squid/Testsuite/x-base-afetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-alistat
++++ b/squid/Testsuite/x-base-alistat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-seqstat
++++ b/squid/Testsuite/x-base-seqstat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sfetch
++++ b/squid/Testsuite/x-base-sfetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-shuffle
++++ b/squid/Testsuite/x-base-shuffle
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sindex
++++ b/squid/Testsuite/x-base-sindex
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sreformat
++++ b/squid/Testsuite/x-base-sreformat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/testsuite/sqc
++++ b/testsuite/sqc
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # sqc 
+ # quality control script for exercising code, regression testing, 
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug  6 11:16:39 2002
+ # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $
+ 
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+ 
+ # Parse our command line
+ #
+-&Getopts('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1;    }
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs,  $opt_r; }
+@@ -506,7 +505,7 @@
+ #
+ sub tempname {
+     my ($dir, $name, $suffix);
+-    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+ 
+     foreach $suffix ("aa".."zz") {
+         $name = "$dir"."sre".$suffix.$$;
+--- a/testsuite/test1-conversion.pl
++++ b/testsuite/test1-conversion.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test hmmconvert.
+ #
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
new file mode 100644
index 000000000000..b9ff5b92b8f9
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
@@ -0,0 +1,89 @@
+Install headers into 'hmmer3' subdir and not into global includedir.
+
+--- a/easel/Makefile.in
++++ b/easel/Makefile.in
+@@ -465,11 +465,12 @@
+ 	${INSTALL} -d ${DESTDIR}${bindir}
+ 	${INSTALL} -d ${DESTDIR}${libdir}
+ 	${INSTALL} -d ${DESTDIR}${includedir}
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/
+ 	for file in ${HDRS}; do\
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+-	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/
++	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/
+ 	${QUIET_SUBDIR0}miniapps      ${QUIET_SUBDIR1} install
+ 
+ # "make uninstall" reverses the steps of "make install"
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -143,6 +143,7 @@
+ 	${INSTALL} -d ${DESTDIR}${bindir}
+ 	${INSTALL} -d ${DESTDIR}${libdir}
+ 	${INSTALL} -d ${DESTDIR}${includedir}
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${INSTALL} -d ${DESTDIR}${man1dir}
+ 	${INSTALL} -d ${DESTDIR}${pdfdir}
+ 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
+--- a/src/impl_dummy/Makefile.in
++++ b/src/impl_dummy/Makefile.in
+@@ -152,8 +152,9 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/impl_sse/Makefile.in
++++ b/src/impl_sse/Makefile.in
+@@ -155,8 +155,9 @@
+ 
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/impl_vmx/Makefile.in
++++ b/src/impl_vmx/Makefile.in
+@@ -152,8 +152,9 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -322,15 +322,16 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install
+ 	for file in ${PROGS}; do \
+ 	   ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\
+ 	done
+ 	${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+-	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\
++	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\
+ 
+ uninstall:
+ 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
new file mode 100644
index 000000000000..39fdbd50e457
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
@@ -0,0 +1,331 @@
+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>
+ #