diff options
Diffstat (limited to 'python-abritamr.spec')
| -rw-r--r-- | python-abritamr.spec | 566 |
1 files changed, 566 insertions, 0 deletions
diff --git a/python-abritamr.spec b/python-abritamr.spec new file mode 100644 index 0000000..2c7e895 --- /dev/null +++ b/python-abritamr.spec @@ -0,0 +1,566 @@ +%global _empty_manifest_terminate_build 0 +Name: python-abritamr +Version: 1.0.14 +Release: 1 +Summary: Running AMRFinderPlus for MDU +License: GNU General Public License v3 (GPLv3) +URL: https://github.com/MDU-PHL/abritamr +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/18/82/01042d0d465d13aed6b904f34d8e9252a3265d0e3c6298fc58820222af42/abritamr-1.0.14.tar.gz +BuildArch: noarch + +Requires: python3-pandas +Requires: python3-xlsxwriter + +%description +<figure><img src="documentation/abriTAMR_logo.jpg"></figure> + +**_logo by Charlie Higgs (PhD candidate)_** + +[](https://circleci.com/gh/MDU-PHL/abritamr) + + +**_Taming the AMR beast_** + +abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. + +_abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia._ + +* Acquired resistance mechanims in the form of point mutations (restricted to subset of species) +* Streamlined output. +* Presence of virulence factors + +## Install + +### Conda + +abritAMR is best installed with `conda` as described below (~2 minutes on laptop) + + +``` +conda create -n abritamr -c bioconda abritamr +conda activate abritamr +``` + +### A note on dependencies + +abriTAMR requires [AMRFinder Plus](https://github.com/ncbi/amr), this can be installed separately with `conda` if required. + +abriTAMR comes packaged with a version of the AMRFinder DB consistent with current NATA accreditation. If you would like to use another DB please download it using `amrfinder -U` and use the `-d` flag to point to your database. + +Current version of AMRFinder Plus compatible with abritAMR 3.10.42 (tested on versions down to 3.10.16) + + + +## Command-line tool + +``` +abritamr run --help + + +optional arguments: + -h, --help show this help message and exit + --contigs CONTIGS, -c CONTIGS + Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig + file (used if only doing a single sample - should provide value for -pfx). (default: ) + --prefix PREFIX, -px PREFIX + If running on a single sample, please provide a prefix for output directory (default: abritamr) + --jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel. (default: 16) + --identity IDENTITY, -i IDENTITY + Set the minimum identity of matches with amrfinder (0 - 1.0). Defaults to amrfinder preset, which is 0.9 + unless a curated threshold is present for the gene. (default: ) + --amrfinder_db AMRFINDER_DB, -d AMRFINDER_DB + Path to amrfinder DB to use (default: + /<path_to_installation>/abritamr/abritamr/db/amrfinderplus/data/2021-09-30.1) + --species {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}, -sp {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes} + Set if you would like to use point mutations, please provide a valid species. (default: ) +``` + +You can also run abriTAMR in `report` mode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (`-q`), with the following columns: + +* ISOLATE +* SPECIES_EXP (the species that was expected) +* SPECIES_OBS (the species that was observed during the quality control analysis) +* TEST_QC (PASS or FAIL) + +`--sop` refers to the type of collation and reporting pipeline +* general + * standard reporting structure for aquired genes, output as reportable and non-reportable +* plus + * Inferred AST based on validation undertaken at MDU + +``` +abritamr report --help + +optional arguments: + -h, --help show this help message and exit + --qc QC, -q QC Name of checked MDU QC file. (default: ) + --runid RUNID, -r RUNID + MDU RunID (default: Run ID) + --matches MATCHES, -m MATCHES + Path to matches, concatentated output of abritamr (default: summary_matches.txt) + --partials PARTIALS, -p PARTIALS + Path to partial matches, concatentated output of abritamr (default: summary_partials.txt) + --sop {general,plus} The MDU pipeline for reporting results. (default: general) +``` + +## Output + +### `abritAMR run` + +Outputs 4 summary files and retains the raw AMRFinderPlus output for each sequence input. + +1. `amrfinder.out` raw output from AMRFinder plus (per sequence). For more information please see AMRFinderPlus help [here](https://github.com/ncbi/amr/wiki/Interpreting-results) + +2. `summary_matches.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Only genes recovered from sequence which have >90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + I. Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + + II. No further annotation indicates that the gene recovered exhibits 100% coverage and 100% identity to a gene in the gene catalog. + + III. Point mutations detected (if `--species` supplied) will also be present in this file in the form of `gene_AAchange`. + +3. `summary_partials.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Genes recovered from sequence which have >50% but <90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + +4. `summary_virulence.txt` + * Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +4. `abritamr.txt` + * Tab-delimited file, combining `summary_matches.txt`, `summary_partials.txt`, `summary_virulence.txt` with a row per sequence, and columns representing AMRFinderPlus virulence gene classification and/or functional drug classes. + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +### `abritamr report` + +will output spreadsheets `general_runid.xlsx` (NATA accredited) or `plus_runid.xlsx` (validated - not yet accredited) depending upon the sop chosen. + +* `general_rundid.xlsx` has two tabs, one for matches and one for partials (corresponding to genes reported in the `summary_matches.txt` and `summary_partials.txt`). Each tab has 7 columns + +| Column | Interpretation | +|:---: | :---: | +| MDU sample ID | Sample ID | +|Item code | suffix (MDU specific) | +| Resistance genes (alleles) detected | genes detected that are reportable (based on species and drug classification)| +| Resistance genes (alleles) det (non-rpt) | other genes detected that are not not reportable for the species detected. +| Species_obs | Species observed (supplied in input file) | +| Species_exp | Species expected (supplied in input file) | +| db_version | Version of the AMRFinderPlus DB used | + +* `plus_runid.xlsx` output is a spreadsheet with the different drug resistance mechanims and the corresponding interpretation (based on validation of genotype and phenotype) for drug-classes relevant to reporting of anti-microbial resistance in _Salmonella enterica_ (other species will be added as validation of genotype vs phenotype is performed). + +* Ampicillin +* Cefotaxime (ESBL) +* Cefotaxime (AmpC) +* Tetracycline +* Gentamicin +* Kanamycin +* Streptomycin +* Sulfathiazole +* Trimethoprim +* Trim-Sulpha +* Chloramphenicol +* Ciprofloxacin +* Meropenem +* Azithromycin +* Aminoglycosides (RMT) +* Colistin + + + + + +%package -n python3-abritamr +Summary: Running AMRFinderPlus for MDU +Provides: python-abritamr +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-abritamr +<figure><img src="documentation/abriTAMR_logo.jpg"></figure> + +**_logo by Charlie Higgs (PhD candidate)_** + +[](https://circleci.com/gh/MDU-PHL/abritamr) + + +**_Taming the AMR beast_** + +abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. + +_abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia._ + +* Acquired resistance mechanims in the form of point mutations (restricted to subset of species) +* Streamlined output. +* Presence of virulence factors + +## Install + +### Conda + +abritAMR is best installed with `conda` as described below (~2 minutes on laptop) + + +``` +conda create -n abritamr -c bioconda abritamr +conda activate abritamr +``` + +### A note on dependencies + +abriTAMR requires [AMRFinder Plus](https://github.com/ncbi/amr), this can be installed separately with `conda` if required. + +abriTAMR comes packaged with a version of the AMRFinder DB consistent with current NATA accreditation. If you would like to use another DB please download it using `amrfinder -U` and use the `-d` flag to point to your database. + +Current version of AMRFinder Plus compatible with abritAMR 3.10.42 (tested on versions down to 3.10.16) + + + +## Command-line tool + +``` +abritamr run --help + + +optional arguments: + -h, --help show this help message and exit + --contigs CONTIGS, -c CONTIGS + Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig + file (used if only doing a single sample - should provide value for -pfx). (default: ) + --prefix PREFIX, -px PREFIX + If running on a single sample, please provide a prefix for output directory (default: abritamr) + --jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel. (default: 16) + --identity IDENTITY, -i IDENTITY + Set the minimum identity of matches with amrfinder (0 - 1.0). Defaults to amrfinder preset, which is 0.9 + unless a curated threshold is present for the gene. (default: ) + --amrfinder_db AMRFINDER_DB, -d AMRFINDER_DB + Path to amrfinder DB to use (default: + /<path_to_installation>/abritamr/abritamr/db/amrfinderplus/data/2021-09-30.1) + --species {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}, -sp {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes} + Set if you would like to use point mutations, please provide a valid species. (default: ) +``` + +You can also run abriTAMR in `report` mode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (`-q`), with the following columns: + +* ISOLATE +* SPECIES_EXP (the species that was expected) +* SPECIES_OBS (the species that was observed during the quality control analysis) +* TEST_QC (PASS or FAIL) + +`--sop` refers to the type of collation and reporting pipeline +* general + * standard reporting structure for aquired genes, output as reportable and non-reportable +* plus + * Inferred AST based on validation undertaken at MDU + +``` +abritamr report --help + +optional arguments: + -h, --help show this help message and exit + --qc QC, -q QC Name of checked MDU QC file. (default: ) + --runid RUNID, -r RUNID + MDU RunID (default: Run ID) + --matches MATCHES, -m MATCHES + Path to matches, concatentated output of abritamr (default: summary_matches.txt) + --partials PARTIALS, -p PARTIALS + Path to partial matches, concatentated output of abritamr (default: summary_partials.txt) + --sop {general,plus} The MDU pipeline for reporting results. (default: general) +``` + +## Output + +### `abritAMR run` + +Outputs 4 summary files and retains the raw AMRFinderPlus output for each sequence input. + +1. `amrfinder.out` raw output from AMRFinder plus (per sequence). For more information please see AMRFinderPlus help [here](https://github.com/ncbi/amr/wiki/Interpreting-results) + +2. `summary_matches.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Only genes recovered from sequence which have >90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + I. Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + + II. No further annotation indicates that the gene recovered exhibits 100% coverage and 100% identity to a gene in the gene catalog. + + III. Point mutations detected (if `--species` supplied) will also be present in this file in the form of `gene_AAchange`. + +3. `summary_partials.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Genes recovered from sequence which have >50% but <90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + +4. `summary_virulence.txt` + * Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +4. `abritamr.txt` + * Tab-delimited file, combining `summary_matches.txt`, `summary_partials.txt`, `summary_virulence.txt` with a row per sequence, and columns representing AMRFinderPlus virulence gene classification and/or functional drug classes. + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +### `abritamr report` + +will output spreadsheets `general_runid.xlsx` (NATA accredited) or `plus_runid.xlsx` (validated - not yet accredited) depending upon the sop chosen. + +* `general_rundid.xlsx` has two tabs, one for matches and one for partials (corresponding to genes reported in the `summary_matches.txt` and `summary_partials.txt`). Each tab has 7 columns + +| Column | Interpretation | +|:---: | :---: | +| MDU sample ID | Sample ID | +|Item code | suffix (MDU specific) | +| Resistance genes (alleles) detected | genes detected that are reportable (based on species and drug classification)| +| Resistance genes (alleles) det (non-rpt) | other genes detected that are not not reportable for the species detected. +| Species_obs | Species observed (supplied in input file) | +| Species_exp | Species expected (supplied in input file) | +| db_version | Version of the AMRFinderPlus DB used | + +* `plus_runid.xlsx` output is a spreadsheet with the different drug resistance mechanims and the corresponding interpretation (based on validation of genotype and phenotype) for drug-classes relevant to reporting of anti-microbial resistance in _Salmonella enterica_ (other species will be added as validation of genotype vs phenotype is performed). + +* Ampicillin +* Cefotaxime (ESBL) +* Cefotaxime (AmpC) +* Tetracycline +* Gentamicin +* Kanamycin +* Streptomycin +* Sulfathiazole +* Trimethoprim +* Trim-Sulpha +* Chloramphenicol +* Ciprofloxacin +* Meropenem +* Azithromycin +* Aminoglycosides (RMT) +* Colistin + + + + + +%package help +Summary: Development documents and examples for abritamr +Provides: python3-abritamr-doc +%description help +<figure><img src="documentation/abriTAMR_logo.jpg"></figure> + +**_logo by Charlie Higgs (PhD candidate)_** + +[](https://circleci.com/gh/MDU-PHL/abritamr) + + +**_Taming the AMR beast_** + +abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. + +_abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia._ + +* Acquired resistance mechanims in the form of point mutations (restricted to subset of species) +* Streamlined output. +* Presence of virulence factors + +## Install + +### Conda + +abritAMR is best installed with `conda` as described below (~2 minutes on laptop) + + +``` +conda create -n abritamr -c bioconda abritamr +conda activate abritamr +``` + +### A note on dependencies + +abriTAMR requires [AMRFinder Plus](https://github.com/ncbi/amr), this can be installed separately with `conda` if required. + +abriTAMR comes packaged with a version of the AMRFinder DB consistent with current NATA accreditation. If you would like to use another DB please download it using `amrfinder -U` and use the `-d` flag to point to your database. + +Current version of AMRFinder Plus compatible with abritAMR 3.10.42 (tested on versions down to 3.10.16) + + + +## Command-line tool + +``` +abritamr run --help + + +optional arguments: + -h, --help show this help message and exit + --contigs CONTIGS, -c CONTIGS + Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig + file (used if only doing a single sample - should provide value for -pfx). (default: ) + --prefix PREFIX, -px PREFIX + If running on a single sample, please provide a prefix for output directory (default: abritamr) + --jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel. (default: 16) + --identity IDENTITY, -i IDENTITY + Set the minimum identity of matches with amrfinder (0 - 1.0). Defaults to amrfinder preset, which is 0.9 + unless a curated threshold is present for the gene. (default: ) + --amrfinder_db AMRFINDER_DB, -d AMRFINDER_DB + Path to amrfinder DB to use (default: + /<path_to_installation>/abritamr/abritamr/db/amrfinderplus/data/2021-09-30.1) + --species {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}, -sp {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes} + Set if you would like to use point mutations, please provide a valid species. (default: ) +``` + +You can also run abriTAMR in `report` mode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (`-q`), with the following columns: + +* ISOLATE +* SPECIES_EXP (the species that was expected) +* SPECIES_OBS (the species that was observed during the quality control analysis) +* TEST_QC (PASS or FAIL) + +`--sop` refers to the type of collation and reporting pipeline +* general + * standard reporting structure for aquired genes, output as reportable and non-reportable +* plus + * Inferred AST based on validation undertaken at MDU + +``` +abritamr report --help + +optional arguments: + -h, --help show this help message and exit + --qc QC, -q QC Name of checked MDU QC file. (default: ) + --runid RUNID, -r RUNID + MDU RunID (default: Run ID) + --matches MATCHES, -m MATCHES + Path to matches, concatentated output of abritamr (default: summary_matches.txt) + --partials PARTIALS, -p PARTIALS + Path to partial matches, concatentated output of abritamr (default: summary_partials.txt) + --sop {general,plus} The MDU pipeline for reporting results. (default: general) +``` + +## Output + +### `abritAMR run` + +Outputs 4 summary files and retains the raw AMRFinderPlus output for each sequence input. + +1. `amrfinder.out` raw output from AMRFinder plus (per sequence). For more information please see AMRFinderPlus help [here](https://github.com/ncbi/amr/wiki/Interpreting-results) + +2. `summary_matches.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Only genes recovered from sequence which have >90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + I. Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + + II. No further annotation indicates that the gene recovered exhibits 100% coverage and 100% identity to a gene in the gene catalog. + + III. Point mutations detected (if `--species` supplied) will also be present in this file in the form of `gene_AAchange`. + +3. `summary_partials.txt` + * Tab-delimited file, with a row per sequence, and columns representing functional drug classes + * Genes recovered from sequence which have >50% but <90% coverage of the gene reported and greater than the desired identity threshold (default 90%). + +4. `summary_virulence.txt` + * Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +4. `abritamr.txt` + * Tab-delimited file, combining `summary_matches.txt`, `summary_partials.txt`, `summary_virulence.txt` with a row per sequence, and columns representing AMRFinderPlus virulence gene classification and/or functional drug classes. + * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). + + * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`. + * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity. + +### `abritamr report` + +will output spreadsheets `general_runid.xlsx` (NATA accredited) or `plus_runid.xlsx` (validated - not yet accredited) depending upon the sop chosen. + +* `general_rundid.xlsx` has two tabs, one for matches and one for partials (corresponding to genes reported in the `summary_matches.txt` and `summary_partials.txt`). Each tab has 7 columns + +| Column | Interpretation | +|:---: | :---: | +| MDU sample ID | Sample ID | +|Item code | suffix (MDU specific) | +| Resistance genes (alleles) detected | genes detected that are reportable (based on species and drug classification)| +| Resistance genes (alleles) det (non-rpt) | other genes detected that are not not reportable for the species detected. +| Species_obs | Species observed (supplied in input file) | +| Species_exp | Species expected (supplied in input file) | +| db_version | Version of the AMRFinderPlus DB used | + +* `plus_runid.xlsx` output is a spreadsheet with the different drug resistance mechanims and the corresponding interpretation (based on validation of genotype and phenotype) for drug-classes relevant to reporting of anti-microbial resistance in _Salmonella enterica_ (other species will be added as validation of genotype vs phenotype is performed). + +* Ampicillin +* Cefotaxime (ESBL) +* Cefotaxime (AmpC) +* Tetracycline +* Gentamicin +* Kanamycin +* Streptomycin +* Sulfathiazole +* Trimethoprim +* Trim-Sulpha +* Chloramphenicol +* Ciprofloxacin +* Meropenem +* Azithromycin +* Aminoglycosides (RMT) +* Colistin + + + + + +%prep +%autosetup -n abritamr-1.0.14 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-abritamr -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.14-1 +- Package Spec generated |