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genometools-genometools: add linux-aarch64 build #47438

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martin-g
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@martin-g
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The Linux ARM64 build fails with the same reasons as:

@mencian mencian added the aarch64 Related to adding linux-aarch64 support label Apr 25, 2024
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g martin-g force-pushed the aarch64-genometools-genometools branch from 9f8d1c5 to 53aff92 Compare April 30, 2024 17:51
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 genometools-genometools-1.6.5-py310h3db02ab_1.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 genometools-genometools-1.6.5-py38hf7b97cc_1.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 genometools-genometools-1.6.5-py39h58cc16e_1.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64 genometools-genometools-1.6.5-py310he54d29d_1.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 genometools-genometools-1.6.5-py38hdd8eff0_1.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 genometools-genometools-1.6.5-py39hb99703e_1.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
linux-aarch64 genometools-genometools-1.6.5-py310h8790e08_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/45731a4b-b19f-434c-9398-f6c9f9dbdf93/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 genometools-genometools-1.6.5-py38h39a79cf_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/45731a4b-b19f-434c-9398-f6c9f9dbdf93/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 genometools-genometools-1.6.5-py39h3edc951_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/45731a4b-b19f-434c-9398-f6c9f9dbdf93/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
genometools-genometools 1.6.5--py310h3db02ab_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/genometools-genometools:1.6.5--py310h3db02ab_1.tar.gz | docker load
genometools-genometools 1.6.5--py38hf7b97cc_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/genometools-genometools:1.6.5--py38hf7b97cc_1.tar.gz | docker load
genometools-genometools 1.6.5--py39h58cc16e_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/genometools-genometools:1.6.5--py39h58cc16e_1.tar.gz | docker load

@aliciaaevans aliciaaevans merged commit 9dde061 into bioconda:master Apr 30, 2024
6 checks passed
@martin-g martin-g deleted the aarch64-genometools-genometools branch May 1, 2024 06:11
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martin-g commented May 1, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/genometools via 🅒 test123 took 17s 
❯ tar xvf genometools-genometools-1.6.5-py310h8790e08_1.tar.bz2                                                                                                                                            (test123) 
info/test/run_test.sh
info/test/run_test.py
info/run_exports.json
info/recipe/build.sh
info/hash_input.json
info/index.json
info/recipe/meta.yaml.template
info/has_prefix
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/licenses/LICENSE
info/files
info/paths.json
info/git
share/genometools/gtdata/modules/gtdoclib/footer_latex.lp
share/genometools/gtdata/modules/gtdoclib/sole_function.lp
share/genometools/gtdata/modules/gtdoclib/libgenometools_header_latex.lp
share/genometools/gtdata/modules/gtdoclib/funcdef.lp
share/genometools/gtdata/modules/gtdoclib/sole_function_latex.lp
share/genometools/gtdata/modules/gtdoclib/module_latex.lp
share/genometools/gtdata/modules/gtdoclib/class.lp
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share/genometools/gtdata/modules/gtdoclib/class_latex.lp
share/genometools/gtdata/modules/gtdoclib/class_comments.lp
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share/genometools/gtdata/modules/gtdoclib/method_latex.lp
share/genometools/gtdata/modules/gtdoclib/modules_latex.lp
share/genometools/gtdata/modules/gtdoclib/classes_latex.lp
share/genometools/gtdata/modules/gtdoclib/libgenometools_header.lp
share/genometools/gtdata/modules/gtdoclib/gtscript_header_latex.lp
share/genometools/gtdata/modules/gtdoclib/gtscript_header.lp
share/genometools/gtdata/doc/csa_example_consensus_spliced_alignments.gff3
share/genometools/gtdata/doc/csa_example_spliced_alignments.gff3
share/genometools/gtdata/sketch/default.style
share/genometools/gtdata/modules/external/des56.lua
share/genometools/gtdata/doc/regionmapping_table.lua
share/genometools/gtdata/doc/select.lua
share/genometools/gtdata/doc/regionmapping_function.lua
share/genometools/gtdata/doc/splicesiteinfo.lua
share/genometools/gtdata/doc/extractfeat.lua
share/genometools/gtdata/doc/id_to_md5.lua
share/genometools/gtdata/doc/snpper.lua
share/genometools/gtdata/doc/cds.lua
share/genometools/gtdata/doc/sequniq.lua
share/genometools/gtdata/doc/luafilter_function.lua
share/genometools/gtdata/doc/readjoiner.lua
share/genometools/gtdata/doc/magicmatch.lua
share/genometools/gtdata/doc/chseqids.lua
share/genometools/gtdata/doc/eval.lua
share/genometools/gtdata/doc/gff3.lua
share/genometools/gtdata/doc/gt.lua
share/genometools/gtdata/modules/external/md5.lua
share/genometools/gtdata/doc/mutate.lua
share/genometools/gtdata/doc/seqmutate.lua
share/genometools/gtdata/doc/luafilter.lua
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share/genometools/gtdata/doc/regionmapping.lua
share/genometools/gtdata/doc/genomediff.lua
share/genometools/gtdata/doc/shredder.lua
share/genometools/gtdata/modules/warning.lua
share/genometools/gtdata/modules/gtlua/range.lua
share/genometools/gtdata/spec/ansicolors.lua
share/genometools/gtdata/modules/stringext.lua
share/genometools/gtdata/doc/csa.lua
share/genometools/gtdata/modules/gtmodulehelper.lua
share/genometools/gtdata/modules/gtdoclib.lua
share/genometools/gtdata/doc/fingerprint.lua
share/genometools/gtdata/modules/gtlua/genome_node.lua
share/genometools/gtdata/modules/external/cgilua/readuntil.lua
share/genometools/gtdata/doc/hop.lua
share/genometools/gtdata/modules/gtlua/helper.lua
share/genometools/gtdata/modules/external/cgilua/dispatcher.lua
share/genometools/gtdata/modules/gtdoclib/docvisitortxt.lua
share/genometools/gtdata/modules/gtlua.lua
share/genometools/gtdata/modules/fileutils.lua
share/genometools/gtdata/doc/extractseq.lua
share/genometools/gtdata/modules/external/cgilua/serialize.lua
share/genometools/gtdata/modules/external/cgilua/cookies.lua
share/genometools/gtdata/modules/external/cgilua/urlcode.lua
share/genometools/gtdata/modules/external/cgilua/loader.lua
share/genometools/gtdata/modules/gtdoclib/docvisitorhtml.lua
share/genometools/gtdata/modules/gtlua/genome_features.lua
share/genometools/gtdata/modules/gtlua/feature_index.lua
share/genometools/gtdata/modules/external/cgilua/lp.lua
share/genometools/gtdata/modules/gtdoclib/docvisitorlatex.lua
share/genometools/gtdata/spec/speclib.lua
share/genometools/gtdata/modules/external/re.lua
share/genometools/gtdata/modules/external/cgilua/mime.lua
share/genometools/gtdata/modules/optparse.lua
share/genometools/gtdata/modules/external/cgilua/session.lua
share/genometools/gtdata/modules/external/cgilua/authentication.lua
share/genometools/gtdata/modules/gtdoclib/docparser.lua
share/genometools/gtdata/modules/external/cgilua/post.lua
share/genometools/gtdata/modules/gtdoclib/docbase.lua
share/genometools/gtdata/modules/external/cgilua/cgilua.lua
include/genometools/core/codon_api.h
include/genometools/annotationsketch/feature_index_api.h
include/genometools/annotationsketch/feature_stream_api.h
include/genometools/annotationsketch/feature_index_memory_api.h
include/genometools/core/endianess_api.h
include/genometools/core/byte_popcount_api.h
include/genometools/extended/reverse_api.h
include/genometools/extended/regular_seqid_api.h
include/genometools/core/class_alloc_api.h
include/genometools/core/strcmp_api.h
include/genometools/extended/type_checker_builtin_api.h
include/genometools/core/unused_api.h
include/genometools/core/qsort_r_api.h
include/genometools/extended/feature_out_stream_api.h
include/genometools/core/md5_fingerprint_api.h
include/genometools/extended/check_boundaries_visitor_api.h
include/genometools/extended/dup_feature_stream_api.h
include/genometools/core/byte_select_api.h
include/genometools/core/multithread_api.h
include/genometools/core/versionfunc_api.h
include/genometools/extended/feature_stream_api.h
include/genometools/extended/gtf_out_stream_api.h
include/genometools/extended/set_source_visitor_api.h
include/genometools/core/init_api.h
include/genometools/extended/sort_stream_api.h
include/genometools/extended/type_checker_obo_api.h
include/genometools/annotationsketch/canvas_api.h
include/genometools/extended/merge_stream_api.h
include/genometools/core/grep_api.h
include/genometools/extended/visitor_stream_api.h
include/genometools/extended/gtf_in_stream_api.h
include/genometools/core/unit_testing_api.h
include/genometools/annotationsketch/custom_track_api.h
include/genometools/extended/merge_feature_stream_api.h
include/genometools/extended/add_introns_stream_api.h
include/genometools/core/symbol_api.h
include/genometools/ltr/ltr_classify_stream_api.h
include/genometools/extended/chain_api.h
include/genometools/core/minmax_api.h
include/genometools/core/msort_api.h
include/genometools/extended/md5_to_id_stream_api.h
include/genometools/core/compat_api.h
include/genometools/extended/gff3_escaping_api.h
include/genometools/core/phase_api.h
include/genometools/extended/csa_stream_api.h
include/genometools/core/fptr_api.h
include/genometools/extended/eof_node_api.h
include/genometools/extended/buffer_stream_api.h
include/genometools/core/codon_iterator_simple_api.h
include/genometools/extended/feature_in_stream_api.h
include/genometools/core/strand_api.h
include/genometools/extended/inter_feature_stream_api.h
include/genometools/core/tooldriver_api.h
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include/genometools/extended/anno_db_schema_api.h
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include/genometools/extended/rdb_sqlite_api.h
include/genometools/core/seq_iterator_sequence_buffer_api.h
include/genometools/extended/id_to_md5_stream_api.h
include/genometools/extended/rdb_visitor_api.h
include/genometools/extended/script_wrapper_stream_api.h
include/genometools/extended/uniq_stream_api.h
include/genometools/extended/feature_index_memory_api.h
include/genometools/extended/xrf_checker_api.h
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include/genometools/annotationsketch/color_api.h
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include/genometools/extended/match_open_api.h
include/genometools/core/md5_seqid_api.h
include/genometools/annotationsketch/text_width_calculator_cairo_api.h
include/genometools/extended/match_iterator_api.h
include/genometools/annotationsketch/custom_track_gc_content_api.h
include/genometools/core/cstr_table_api.h
include/genometools/annotationsketch/text_width_calculator_api.h
include/genometools/core/bsearch_api.h
include/genometools/extended/splice_site_info_stream_api.h
include/genometools/annotationsketch/canvas_cairo_context_api.h
include/genometools/core/basename_api.h
include/genometools/core/str_cache_api.h
include/genometools/core/warning_api.h
include/genometools/core/md5_encoder_api.h
include/genometools/core/queue_api.h
include/genometools/extended/match_last_api.h
include/genometools/ltr/ltr_cluster_stream_api.h
include/genometools/core/ensure_api.h
include/genometools/core/countingsort_api.h
include/genometools/extended/region_node_api.h
include/genometools/extended/feature_node_iterator_api.h
include/genometools/core/seq_iterator_fastq_api.h
include/genometools/core/toolbox_api.h
include/genometools/extended/bed_in_stream_api.h
include/genometools/annotationsketch/image_info_api.h
include/genometools/extended/gff3_visitor_api.h
include/genometools/extended/comment_node_api.h
include/genometools/core/orf_api.h
include/genometools/extended/type_checker_api.h
include/genometools/core/cstr_api.h
include/genometools/extended/gff3_out_stream_api.h
include/genometools/core/seq_api.h
include/genometools/core/array2dim_sparse_api.h
include/genometools/core/output_file_api.h
include/genometools/core/bool_matrix_api.h
include/genometools/core/codon_iterator_encseq_api.h
include/genometools/core/splitter_api.h
include/genometools/extended/match_sw_api.h
include/genometools/extended/cds_stream_api.h
include/genometools/annotationsketch/canvas_cairo_file_api.h
include/genometools/extended/meta_node_api.h
include/genometools/extended/stat_stream_api.h
include/genometools/core/yarandom_api.h
include/genometools/annotationsketch/graphics_cairo_api.h
include/genometools/core/divmodmul_api.h
include/genometools/core/fasta_reader_api.h
include/genometools/core/logger_api.h
include/genometools/extended/cds_visitor_api.h
include/genometools/extended/script_wrapper_visitor_api.h
include/genometools/annotationsketch/custom_track_script_wrapper_api.h
include/genometools/extended/consensus_sa_api.h
include/genometools/extended/script_filter_api.h
include/genometools/core/assert_api.h
include/genometools/annotationsketch/rec_map_api.h
include/genometools/extended/sequence_node_api.h
include/genometools/extended/orf_iterator_api.h
include/genometools/extended/feature_type_api.h
include/genometools/core/score_matrix_api.h
include/genometools/extended/extract_feature_stream_api.h
include/genometools/extended/seqid2file_api.h
include/genometools/core/str_array_api.h
include/genometools/core/disc_distri_api.h
include/genometools/core/mathsupport_api.h
include/genometools/extended/rdb_api.h
include/genometools/core/dlist_api.h
include/genometools/core/array2dim_api.h
include/genometools/core/xposix_api.h
include/genometools/core/codon_iterator_api.h
include/genometools/extended/globalchaining_api.h
include/genometools/core/seq_iterator_api.h
include/genometools/core/trans_table_api.h
include/genometools/core/types_api.h
include/genometools/core/error_api.h
include/genometools/core/md5_tab_api.h
include/genometools/core/thread_api.h
include/genometools/core/parseutils_api.h
include/genometools/core/xansi_api.h
include/genometools/extended/gff3_in_stream_api.h
include/genometools/annotationsketch/diagram_api.h
include/genometools/annotationsketch/block_api.h
include/genometools/core/ma_api.h
include/genometools/extended/tag_value_map_api.h
include/genometools/core/timer_api.h
include/genometools/ltr/ltr_refseq_match_stream_api.h
include/genometools/core/chardef_api.h
include/genometools/annotationsketch/layout_api.h
include/genometools/core/bittab_api.h
include/genometools/core/str_api.h
include/genometools/extended/match_api.h
include/genometools/extended/node_visitor_api.h
include/genometools/extended/match_blast_api.h
include/genometools/core/tool_api.h
include/genometools/extended/select_stream_api.h
include/genometools/core/hashmap_api.h
include/genometools/core/fileutils_api.h
include/genometools/core/file_api.h
include/genometools/core/interval_tree_api.h
include/genometools/extended/genome_node_api.h
include/genometools/core/arraydef_api.h
include/genometools/extended/node_stream_api.h
include/genometools/extended/gff3_parser_api.h
include/genometools/core/array3dim_api.h
include/genometools/core/array_api.h
include/genometools/core/fasta_api.h
include/genometools/core/translator_api.h
include/genometools/extended/region_mapping_api.h
include/genometools/extended/rbtree_api.h
include/genometools/core/range_api.h
include/genometools/extended/feature_index_api.h
include/genometools/core/bioseq_api.h
include/genometools/genometools.h
include/genometools/core/alphabet_api.h
include/genometools/annotationsketch/graphics_api.h
include/genometools/annotationsketch/style_api.h
include/genometools/gt_config.h
include/genometools/core/fa_api.h
include/genometools/core/safearith_api.h
include/genometools/extended/feature_node_api.h
include/genometools/core/option_api.h
include/genometools/core/encseq_api.h
share/genometools/gtdata/obo_files/sofa.obo
share/genometools/gtdata/obo_files/so.obo
share/genometools/gtdata/obo_files/so-xp.obo
share/genometools/gtdata/trans/Transab
share/genometools/gtdata/trans/TransDNA
share/genometools/gtdata/trans/TransDNAlowermask
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share/genometools/gtdata/trans/TransDNA_CBNP
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share/genometools/gtdata/trans/TransProt11
share/genometools/gtdata/trans/TransMass
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share/genometools/gtdata/trans/TransProt12
share/genometools/gtdata/trans/TransProtall
share/genometools/gtdata/obo_files/README
lib/libgenometools.so
share/genometools/gtdata/xrf_abbr/GO.xrf_abbr
lib/python3.10/site-packages/GenomeTools.pth
bin/genometools-config
bin/gt
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/output_drivers/json
share/genometools/gtdata/spec/output_drivers/html
lib/python3.10/site-packages/GenomeTools-1.6.5-py3.10.egg
lib/libgenometools.a

mgrigorov in 🌐 euler-arm-22 in /tmp/genometools via 🅒 test123 took 2s 
❯ file ./bin/*                                                                                                                                                                                             (test123) 
./bin/genometools-config: POSIX shell script, ASCII text executable, with very long lines (1204)
./bin/gt:                 ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/genometools via 🅒 test123 
❯ ./bin/gt                                                                                                                                                                                                 (test123) 
./bin/gt: error: neither tool nor script specified; option -help lists possible tools

mgrigorov in 🌐 euler-arm-22 in /tmp/genometools via 🅒 test123 
❯ ./bin/gt --help                                                                                                                                                                                          (test123) 
Usage: ./bin/gt [option ...] [tool | script] [argument ...]
The GenomeTools genome analysis system.

-i       enter interactive mode after executing 'tool' or 'script'
-q       suppress warnings
-test    perform unit tests and exit
-seed    set seed for random number generator manually.
         0 generates a seed from current time and process id
-help    display help and exit
-version display version information and exit

Tools:

bed_to_gff3
cds
chain2dim
chseqids
clean
compreads
condenseq
congruence
convertseq
csa
dot
dupfeat
encseq
encseq2spm
eval
extractfeat
extractseq
fastq_sample
featureindex
fingerprint
genomediff
gff3
gff3_to_gtf
gff3validator
gtf_to_gff3
hop
id_to_md5
inlineseq_add
inlineseq_split
interfeat
loccheck
ltrclustering
ltrdigest
ltrharvest
matchtool
matstat
md5_to_id
merge
mergefeat
mgth
mkfeatureindex
mkfmindex
mmapandread
orffinder
packedindex
prebwt
readjoiner
repfind
scriptfilter
seed_extend
select
seq
seqfilter
seqids
seqmutate
seqorder
seqstat
seqtransform
seqtranslate
sequniq
shredder
shulengthdist
simreads
sketch
sketch_page
snpper
speck
splicesiteinfo
splitfasta
stat
suffixerator
tagerator
tallymer
tirvish
uniq
uniquesub
wtree

Set the environment variable `GT_MEM_BOOKKEEPING=on` to enable memory
bookkeeping (e.g., like this: `env GT_MEM_BOOKKEEPING=on gt`).

Set the environment variable `GT_ENV_OPTIONS=-spacepeak` to show a spacepeak
after program run.
Set the environment variable `GT_ENV_OPTIONS=-showtime` to show processing times
for some program parts if implemented.

Set the environment variable `GT_SEED` to an integer value to supply a seed for
the random number generator. Can be overridden by the `-seed` option.

Combinations are possible. Running the `gt` binary with `GT_ENV_OPTIONS=-help`
shows all possible "environment options".

Report bugs to https://github.com/genometools/genometools/issues.

LGTM!

daler pushed a commit that referenced this pull request May 14, 2024
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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