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genometools: Import genometools-1.6.2 as wip/genometools.

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Wed Sep 15 13:49:40 2021 -0600
Changeset:	2f20318d9bf38ccf06711b957919476725ca2c3a

Modified Files:
	Makefile
Added Files:
	genometools/DESCR
	genometools/Makefile
	genometools/PLIST
	genometools/TODO
	genometools/distinfo
	genometools/patches/patch-Makefile
	genometools/patches/patch-scripts_calltestcase.sh
	genometools/patches/patch-scripts_spmcheck.sh

Log Message:
genometools: Import genometools-1.6.2 as wip/genometools.

The GenomeTools genome analysis system is a free collection of
bioinformatics tools (in the realm of genome informatics) combined
into a single binary named `gt`. It is based on a C library named
`libgenometools` which contains a wide variety of classes for
efficient and convenient implementation of sequence and annotation
processing software.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2f20318d9bf38ccf06711b957919476725ca2c3a

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                          |   1 +
 genometools/DESCR                                 |   6 +
 genometools/Makefile                              |  26 ++
 genometools/PLIST                                 | 321 ++++++++++++++++++++++
 genometools/TODO                                  |   6 +
 genometools/distinfo                              |   9 +
 genometools/patches/patch-Makefile                |  17 ++
 genometools/patches/patch-scripts_calltestcase.sh |  16 ++
 genometools/patches/patch-scripts_spmcheck.sh     |  16 ++
 9 files changed, 418 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 5254f7aa1c..2d4539e3b7 100644
--- a/Makefile
+++ b/Makefile
@@ -1091,6 +1091,7 @@ SUBDIR+=	geekcode
 SUBDIR+=	gemma
 SUBDIR+=	generand
 SUBDIR+=	geners
+SUBDIR+=	genometools
 SUBDIR+=	genus2reduction
 SUBDIR+=	geoloc
 SUBDIR+=	gerbera
diff --git a/genometools/DESCR b/genometools/DESCR
new file mode 100644
index 0000000000..83f6fc9a69
--- /dev/null
+++ b/genometools/DESCR
@@ -0,0 +1,6 @@
+The GenomeTools genome analysis system is a free collection of
+bioinformatics tools (in the realm of genome informatics) combined
+into a single binary named `gt`. It is based on a C library named
+`libgenometools` which contains a wide variety of classes for
+efficient and convenient implementation of sequence and annotation
+processing software.
diff --git a/genometools/Makefile b/genometools/Makefile
new file mode 100644
index 0000000000..0e1aa1ba2b
--- /dev/null
+++ b/genometools/Makefile
@@ -0,0 +1,26 @@
+# $NetBSD$
+
+DISTNAME=	genometools-1.6.2
+CATEGORIES=	biology
+MASTER_SITES=	http://genometools.org/pub/
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	http://genometools.org/pub/
+COMMENT=	Collection of bioinformatics tools
+LICENSE=	isc # + others for specific external tools
+
+USE_TOOLS+=	gmake pkg-config
+USE_LANGUAGES+=	c
+# MAKE_ENV+=	useshared=yes	# include system libraries, but need dependencies
+INSTALL_ENV+=	prefix=${PREFIX}
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OS} == Darwin
+pre-install:
+	install_name_tool -id ${PREFIX}/lib/libgenometools.dylib ${WRKSRC}/lib/libgenometools.dylib
+.endif
+
+.include "../../devel/pango/buildlink3.mk"
+.include "../../graphics/cairo/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/genometools/PLIST b/genometools/PLIST
new file mode 100644
index 0000000000..a6b07dbeca
--- /dev/null
+++ b/genometools/PLIST
@@ -0,0 +1,321 @@
+@comment $NetBSD$
+bin/genometools-config
+bin/gt
+include/genometools/annotationsketch/block_api.h
+include/genometools/annotationsketch/canvas_api.h
+include/genometools/annotationsketch/canvas_cairo_context_api.h
+include/genometools/annotationsketch/canvas_cairo_file_api.h
+include/genometools/annotationsketch/color_api.h
+include/genometools/annotationsketch/custom_track_api.h
+include/genometools/annotationsketch/custom_track_gc_content_api.h
+include/genometools/annotationsketch/custom_track_script_wrapper_api.h
+include/genometools/annotationsketch/diagram_api.h
+include/genometools/annotationsketch/feature_index_api.h
+include/genometools/annotationsketch/feature_index_memory_api.h
+include/genometools/annotationsketch/feature_stream_api.h
+include/genometools/annotationsketch/graphics_api.h
+include/genometools/annotationsketch/graphics_cairo_api.h
+include/genometools/annotationsketch/image_info_api.h
+include/genometools/annotationsketch/layout_api.h
+include/genometools/annotationsketch/rec_map_api.h
+include/genometools/annotationsketch/style_api.h
+include/genometools/annotationsketch/text_width_calculator_api.h
+include/genometools/annotationsketch/text_width_calculator_cairo_api.h
+include/genometools/core/alphabet_api.h
+include/genometools/core/array2dim_api.h
+include/genometools/core/array2dim_sparse_api.h
+include/genometools/core/array3dim_api.h
+include/genometools/core/array_api.h
+include/genometools/core/arraydef_api.h
+include/genometools/core/assert_api.h
+include/genometools/core/basename_api.h
+include/genometools/core/bioseq_api.h
+include/genometools/core/bittab_api.h
+include/genometools/core/bool_matrix_api.h
+include/genometools/core/bsearch_api.h
+include/genometools/core/byte_popcount_api.h
+include/genometools/core/byte_select_api.h
+include/genometools/core/chardef_api.h
+include/genometools/core/class_alloc_api.h
+include/genometools/core/codon_api.h
+include/genometools/core/codon_iterator_api.h
+include/genometools/core/codon_iterator_encseq_api.h
+include/genometools/core/codon_iterator_simple_api.h
+include/genometools/core/compat_api.h
+include/genometools/core/countingsort_api.h
+include/genometools/core/cstr_api.h
+include/genometools/core/cstr_array_api.h
+include/genometools/core/cstr_table_api.h
+include/genometools/core/deprecated_api.h
+include/genometools/core/disc_distri_api.h
+include/genometools/core/divmodmul_api.h
+include/genometools/core/dlist_api.h
+include/genometools/core/encseq_api.h
+include/genometools/core/endianess_api.h
+include/genometools/core/ensure_api.h
+include/genometools/core/error_api.h
+include/genometools/core/fa_api.h
+include/genometools/core/fasta_api.h
+include/genometools/core/fasta_reader_api.h
+include/genometools/core/file_api.h
+include/genometools/core/fileutils_api.h
+include/genometools/core/fptr_api.h
+include/genometools/core/grep_api.h
+include/genometools/core/hashmap_api.h
+include/genometools/core/init_api.h
+include/genometools/core/interval_tree_api.h
+include/genometools/core/log_api.h
+include/genometools/core/logger_api.h
+include/genometools/core/ma_api.h
+include/genometools/core/mathsupport_api.h
+include/genometools/core/md5_encoder_api.h
+include/genometools/core/md5_fingerprint_api.h
+include/genometools/core/md5_seqid_api.h
+include/genometools/core/md5_tab_api.h
+include/genometools/core/minmax_api.h
+include/genometools/core/msort_api.h
+include/genometools/core/multithread_api.h
+include/genometools/core/option_api.h
+include/genometools/core/orf_api.h
+include/genometools/core/output_file_api.h
+include/genometools/core/parseutils_api.h
+include/genometools/core/phase_api.h
+include/genometools/core/qsort_r_api.h
+include/genometools/core/queue_api.h
+include/genometools/core/range_api.h
+include/genometools/core/readmode_api.h
+include/genometools/core/safearith_api.h
+include/genometools/core/score_matrix_api.h
+include/genometools/core/seq_api.h
+include/genometools/core/seq_iterator_api.h
+include/genometools/core/seq_iterator_fastq_api.h
+include/genometools/core/seq_iterator_sequence_buffer_api.h
+include/genometools/core/splitter_api.h
+include/genometools/core/str_api.h
+include/genometools/core/str_array_api.h
+include/genometools/core/str_cache_api.h
+include/genometools/core/strand_api.h
+include/genometools/core/strcmp_api.h
+include/genometools/core/symbol_api.h
+include/genometools/core/thread_api.h
+include/genometools/core/timer_api.h
+include/genometools/core/tool_api.h
+include/genometools/core/toolbox_api.h
+include/genometools/core/tooldriver_api.h
+include/genometools/core/trans_table_api.h
+include/genometools/core/translator_api.h
+include/genometools/core/types_api.h
+include/genometools/core/undef_api.h
+include/genometools/core/unit_testing_api.h
+include/genometools/core/unused_api.h
+include/genometools/core/version_api.h
+include/genometools/core/versionfunc_api.h
+include/genometools/core/warning_api.h
+include/genometools/core/xansi_api.h
+include/genometools/core/xposix_api.h
+include/genometools/core/yarandom_api.h
+include/genometools/extended/add_introns_stream_api.h
+include/genometools/extended/anno_db_gfflike_api.h
+include/genometools/extended/anno_db_schema_api.h
+include/genometools/extended/array_in_stream_api.h
+include/genometools/extended/array_out_stream_api.h
+include/genometools/extended/bed_in_stream_api.h
+include/genometools/extended/buffer_stream_api.h
+include/genometools/extended/cds_stream_api.h
+include/genometools/extended/cds_visitor_api.h
+include/genometools/extended/chain_api.h
+include/genometools/extended/check_boundaries_visitor_api.h
+include/genometools/extended/comment_node_api.h
+include/genometools/extended/consensus_sa_api.h
+include/genometools/extended/csa_stream_api.h
+include/genometools/extended/dup_feature_stream_api.h
+include/genometools/extended/eof_node_api.h
+include/genometools/extended/extract_feature_stream_api.h
+include/genometools/extended/feature_in_stream_api.h
+include/genometools/extended/feature_index_api.h
+include/genometools/extended/feature_index_memory_api.h
+include/genometools/extended/feature_node_api.h
+include/genometools/extended/feature_node_iterator_api.h
+include/genometools/extended/feature_out_stream_api.h
+include/genometools/extended/feature_stream_api.h
+include/genometools/extended/feature_type_api.h
+include/genometools/extended/genome_node_api.h
+include/genometools/extended/gff3_escaping_api.h
+include/genometools/extended/gff3_in_stream_api.h
+include/genometools/extended/gff3_out_stream_api.h
+include/genometools/extended/gff3_parser_api.h
+include/genometools/extended/gff3_visitor_api.h
+include/genometools/extended/globalchaining_api.h
+include/genometools/extended/gtf_in_stream_api.h
+include/genometools/extended/gtf_out_stream_api.h
+include/genometools/extended/id_to_md5_stream_api.h
+include/genometools/extended/inter_feature_stream_api.h
+include/genometools/extended/match_api.h
+include/genometools/extended/match_blast_api.h
+include/genometools/extended/match_iterator_api.h
+include/genometools/extended/match_last_api.h
+include/genometools/extended/match_open_api.h
+include/genometools/extended/match_sw_api.h
+include/genometools/extended/match_visitor_api.h
+include/genometools/extended/md5_to_id_stream_api.h
+include/genometools/extended/merge_feature_stream_api.h
+include/genometools/extended/merge_stream_api.h
+include/genometools/extended/meta_node_api.h
+include/genometools/extended/node_stream_api.h
+include/genometools/extended/node_visitor_api.h
+include/genometools/extended/orf_iterator_api.h
+include/genometools/extended/rbtree_api.h
+include/genometools/extended/rdb_api.h
+include/genometools/extended/rdb_mysql_api.h
+include/genometools/extended/rdb_sqlite_api.h
+include/genometools/extended/rdb_visitor_api.h
+include/genometools/extended/region_mapping_api.h
+include/genometools/extended/region_node_api.h
+include/genometools/extended/regular_seqid_api.h
+include/genometools/extended/reverse_api.h
+include/genometools/extended/script_filter_api.h
+include/genometools/extended/script_wrapper_stream_api.h
+include/genometools/extended/script_wrapper_visitor_api.h
+include/genometools/extended/select_stream_api.h
+include/genometools/extended/seqid2file_api.h
+include/genometools/extended/sequence_node_api.h
+include/genometools/extended/set_source_visitor_api.h
+include/genometools/extended/sort_stream_api.h
+include/genometools/extended/splice_site_info_stream_api.h
+include/genometools/extended/stat_stream_api.h
+include/genometools/extended/tag_value_map_api.h
+include/genometools/extended/type_checker_api.h
+include/genometools/extended/type_checker_builtin_api.h
+include/genometools/extended/type_checker_obo_api.h
+include/genometools/extended/uniq_stream_api.h
+include/genometools/extended/visitor_stream_api.h
+include/genometools/extended/xrf_checker_api.h
+include/genometools/genometools.h
+include/genometools/gt_config.h
+include/genometools/ltr/ltr_classify_stream_api.h
+include/genometools/ltr/ltr_cluster_stream_api.h
+include/genometools/ltr/ltr_orf_annotator_stream_api.h
+include/genometools/ltr/ltr_refseq_match_stream_api.h
+lib/libgenometools.a
+lib/libgenometools.dylib
+share/genometools/gtdata/doc/cds.lua
+share/genometools/gtdata/doc/chseqids.lua
+share/genometools/gtdata/doc/csa.lua
+share/genometools/gtdata/doc/csa_example_consensus_spliced_alignments.gff3
+share/genometools/gtdata/doc/csa_example_spliced_alignments.gff3
+share/genometools/gtdata/doc/eval.lua
+share/genometools/gtdata/doc/extractfeat.lua
+share/genometools/gtdata/doc/extractseq.lua
+share/genometools/gtdata/doc/fingerprint.lua
+share/genometools/gtdata/doc/genomediff.lua
+share/genometools/gtdata/doc/gff3.lua
+share/genometools/gtdata/doc/gt.lua
+share/genometools/gtdata/doc/hop.lua
+share/genometools/gtdata/doc/id_to_md5.lua
+share/genometools/gtdata/doc/luafilter.lua
+share/genometools/gtdata/doc/luafilter_function.lua
+share/genometools/gtdata/doc/magicmatch.lua
+share/genometools/gtdata/doc/mutate.lua
+share/genometools/gtdata/doc/readjoiner.lua
+share/genometools/gtdata/doc/regionmapping.lua
+share/genometools/gtdata/doc/regionmapping_function.lua
+share/genometools/gtdata/doc/regionmapping_table.lua
+share/genometools/gtdata/doc/select.lua
+share/genometools/gtdata/doc/seqmutate.lua
+share/genometools/gtdata/doc/sequniq.lua
+share/genometools/gtdata/doc/shredder.lua
+share/genometools/gtdata/doc/snpper.lua
+share/genometools/gtdata/doc/splicesiteinfo.lua
+share/genometools/gtdata/doc/uniq.lua
+share/genometools/gtdata/modules/external/cgilua/authentication.lua
+share/genometools/gtdata/modules/external/cgilua/cgilua.lua
+share/genometools/gtdata/modules/external/cgilua/cookies.lua
+share/genometools/gtdata/modules/external/cgilua/dispatcher.lua
+share/genometools/gtdata/modules/external/cgilua/loader.lua
+share/genometools/gtdata/modules/external/cgilua/lp.lua
+share/genometools/gtdata/modules/external/cgilua/mime.lua
+share/genometools/gtdata/modules/external/cgilua/post.lua
+share/genometools/gtdata/modules/external/cgilua/readuntil.lua
+share/genometools/gtdata/modules/external/cgilua/serialize.lua
+share/genometools/gtdata/modules/external/cgilua/session.lua
+share/genometools/gtdata/modules/external/cgilua/urlcode.lua
+share/genometools/gtdata/modules/external/des56.lua
+share/genometools/gtdata/modules/external/md5.lua
+share/genometools/gtdata/modules/external/re.lua
+share/genometools/gtdata/modules/fileutils.lua
+share/genometools/gtdata/modules/gtdoclib.lua
+share/genometools/gtdata/modules/gtdoclib/class.lp
+share/genometools/gtdata/modules/gtdoclib/class_comments.lp
+share/genometools/gtdata/modules/gtdoclib/class_comments_latex.lp
+share/genometools/gtdata/modules/gtdoclib/class_latex.lp
+share/genometools/gtdata/modules/gtdoclib/classes.lp
+share/genometools/gtdata/modules/gtdoclib/classes_latex.lp
+share/genometools/gtdata/modules/gtdoclib/docbase.lua
+share/genometools/gtdata/modules/gtdoclib/docparser.lua
+share/genometools/gtdata/modules/gtdoclib/docvisitorhtml.lua
+share/genometools/gtdata/modules/gtdoclib/docvisitorlatex.lua
+share/genometools/gtdata/modules/gtdoclib/docvisitortxt.lua
+share/genometools/gtdata/modules/gtdoclib/footer.lp
+share/genometools/gtdata/modules/gtdoclib/footer_latex.lp
+share/genometools/gtdata/modules/gtdoclib/funcdef.lp
+share/genometools/gtdata/modules/gtdoclib/funcdef_latex.lp
+share/genometools/gtdata/modules/gtdoclib/gtscript_header.lp
+share/genometools/gtdata/modules/gtdoclib/gtscript_header_latex.lp
+share/genometools/gtdata/modules/gtdoclib/index.lp
+share/genometools/gtdata/modules/gtdoclib/libgenometools_header.lp
+share/genometools/gtdata/modules/gtdoclib/libgenometools_header_latex.lp
+share/genometools/gtdata/modules/gtdoclib/method.lp
+share/genometools/gtdata/modules/gtdoclib/method_latex.lp
+share/genometools/gtdata/modules/gtdoclib/module.lp
+share/genometools/gtdata/modules/gtdoclib/module_latex.lp
+share/genometools/gtdata/modules/gtdoclib/modules.lp
+share/genometools/gtdata/modules/gtdoclib/modules_latex.lp
+share/genometools/gtdata/modules/gtdoclib/sole_function.lp
+share/genometools/gtdata/modules/gtdoclib/sole_function_latex.lp
+share/genometools/gtdata/modules/gtdoclib/variable.lp
+share/genometools/gtdata/modules/gtdoclib/variable_latex.lp
+share/genometools/gtdata/modules/gtlua.lua
+share/genometools/gtdata/modules/gtlua/feature_index.lua
+share/genometools/gtdata/modules/gtlua/genome_features.lua
+share/genometools/gtdata/modules/gtlua/genome_node.lua
+share/genometools/gtdata/modules/gtlua/helper.lua
+share/genometools/gtdata/modules/gtlua/range.lua
+share/genometools/gtdata/modules/gtmodulehelper.lua
+share/genometools/gtdata/modules/optparse.lua
+share/genometools/gtdata/modules/stringext.lua
+share/genometools/gtdata/modules/warning.lua
+share/genometools/gtdata/obo_files/README
+share/genometools/gtdata/obo_files/so-xp.obo
+share/genometools/gtdata/obo_files/so.obo
+share/genometools/gtdata/obo_files/sofa.obo
+share/genometools/gtdata/sketch/default.style
+share/genometools/gtdata/spec/ansicolors.lua
+share/genometools/gtdata/spec/output_drivers/html
+share/genometools/gtdata/spec/output_drivers/json
+share/genometools/gtdata/spec/output_drivers/statsonly
+share/genometools/gtdata/spec/output_drivers/tabular
+share/genometools/gtdata/spec/output_drivers/text
+share/genometools/gtdata/spec/speclib.lua
+share/genometools/gtdata/trans/TransAnum
+share/genometools/gtdata/trans/TransDNA
+share/genometools/gtdata/trans/TransDNAX
+share/genometools/gtdata/trans/TransDNAX2
+share/genometools/gtdata/trans/TransDNA_CBNP
+share/genometools/gtdata/trans/TransDNAall
+share/genometools/gtdata/trans/TransDNAlowermask
+share/genometools/gtdata/trans/TransMass
+share/genometools/gtdata/trans/TransProt11
+share/genometools/gtdata/trans/TransProt12
+share/genometools/gtdata/trans/TransProt2
+share/genometools/gtdata/trans/TransProt20
+share/genometools/gtdata/trans/TransProt21
+share/genometools/gtdata/trans/TransProt3
+share/genometools/gtdata/trans/TransProt3B
+share/genometools/gtdata/trans/TransProt4
+share/genometools/gtdata/trans/TransProt4B
+share/genometools/gtdata/trans/TransProt6
+share/genometools/gtdata/trans/TransProt7
+share/genometools/gtdata/trans/TransProt8
+share/genometools/gtdata/trans/TransProtall
+share/genometools/gtdata/trans/Transab
+share/genometools/gtdata/xrf_abbr/GO.xrf_abbr
diff --git a/genometools/TODO b/genometools/TODO
new file mode 100644
index 0000000000..2a52fd7919
--- /dev/null
+++ b/genometools/TODO
@@ -0,0 +1,6 @@
+TODO
+
+- the LICENSE file has many listed for all the external tools; how
+  should this be handled?
+
+- use pkgsrc dependencies instead of bundled software
diff --git a/genometools/distinfo b/genometools/distinfo
new file mode 100644
index 0000000000..768e7db052
--- /dev/null
+++ b/genometools/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+SHA1 (genometools-1.6.2.tar.gz) = 028d4cff1e75280497ac650b45b782d815166eef
+RMD160 (genometools-1.6.2.tar.gz) = 941f8508f2498383e87a95df8ae6a171e0021ec2
+SHA512 (genometools-1.6.2.tar.gz) = 02b558d9a7d2bf75603bd8a620b669e010586eb9217ea031b46e0441dd9b2188687916e9c9bb5ffde8b3ffe9171f589632ebd41aa963a38837073e1a633b7c75
+Size (genometools-1.6.2.tar.gz) = 13731845 bytes
+SHA1 (patch-Makefile) = 5ca4fd4f44ed8efcbe2c859f19d52ee87b28a0f6
+SHA1 (patch-scripts_calltestcase.sh) = f73793e66c8f2884e7eddb96117aab2532737c00
+SHA1 (patch-scripts_spmcheck.sh) = e89f13a4818ee28e3b8fd686a7c4d1471d1b6c2a
diff --git a/genometools/patches/patch-Makefile b/genometools/patches/patch-Makefile
new file mode 100644
index 0000000000..56109c25ca
--- /dev/null
+++ b/genometools/patches/patch-Makefile
@@ -0,0 +1,17 @@
+$NetBSD$
+
+Do not override PKG_CONFIG_PATH to find pkgsrc dependencies.
+
+--- Makefile.orig	2021-06-24 14:43:03.000000000 +0000
++++ Makefile
+@@ -21,8 +21,8 @@ INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/
+ ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0)
+   HAS_PKGCONFIG:=yes
+   # Fix for Mac OS X manual building with Homebrew
+-  OLD_PKG_CONFIG_PATH:=$(PKG_CONFIG_PATH)
+-  OVERRIDE_PC_PATH:=PKG_CONFIG_PATH=$(OLD_PKG_CONFIG_PATH):/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig
++  # OLD_PKG_CONFIG_PATH:=$(PKG_CONFIG_PATH)
++  # OVERRIDE_PC_PATH:=PKG_CONFIG_PATH=$(OLD_PKG_CONFIG_PATH):/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig
+ else
+   HAS_PKGCONFIG:=no
+ endif
diff --git a/genometools/patches/patch-scripts_calltestcase.sh b/genometools/patches/patch-scripts_calltestcase.sh
new file mode 100644
index 0000000000..a7e82e76c0
--- /dev/null
+++ b/genometools/patches/patch-scripts_calltestcase.sh
@@ -0,0 +1,16 @@
+$NetBSD$
+
+Improve portability of test usage.  Reported upstream as
+https://github.com/genometools/genometools/issues/989.
+
+--- scripts/calltestcase.sh.orig	2021-06-24 14:43:03.000000000 +0000
++++ scripts/calltestcase.sh
+@@ -2,7 +2,7 @@
+ 
+ cd testsuite
+ 
+-if test "${TMPDIR}" == ""
++if test "${TMPDIR}" = ""
+ then
+   TMPDIR="."
+ fi
diff --git a/genometools/patches/patch-scripts_spmcheck.sh b/genometools/patches/patch-scripts_spmcheck.sh
new file mode 100644
index 0000000000..bf371716b9
--- /dev/null
+++ b/genometools/patches/patch-scripts_spmcheck.sh
@@ -0,0 +1,16 @@
+$NetBSD$
+
+Improve portability of test usage.  Reported upstream as
+https://github.com/genometools/genometools/issues/989.
+
+--- scripts/spmcheck.sh.orig	2021-06-24 14:43:03.000000000 +0000
++++ scripts/spmcheck.sh
+@@ -14,7 +14,7 @@ inputfile=$3
+ 
+ env -i bin/gt sequniq -rev $inputfile > tmp.fas
+ sfxopt="-pl 2 -dna -lcp -suf -tis -ssp -db tmp.fas"
+-if test ${mirrored} == "m"
++if test ${mirrored} = "m"
+ then
+   idx="sfx-m"
+ else
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