diff options
Diffstat (limited to 'python-mycotools.spec')
| -rw-r--r-- | python-mycotools.spec | 240 |
1 files changed, 240 insertions, 0 deletions
diff --git a/python-mycotools.spec b/python-mycotools.spec new file mode 100644 index 0000000..e8c5be7 --- /dev/null +++ b/python-mycotools.spec @@ -0,0 +1,240 @@ +%global _empty_manifest_terminate_build 0 +Name: python-mycotools +Version: 0.27.36 +Release: 1 +Summary: A compilation of bioinformatic and computation biology inspired python tools +License: GNU Lesser General Public License v3 or later (LGPLv3+) +URL: https://gitlab.com/xonq/mycotools/mycotools +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/97/9e/8fde0cbb9cedd95e9d1b89137708f36fc9ea8f5f631bf5485637c952305b/mycotools-0.27.36.tar.gz +BuildArch: noarch + +Requires: python3-biopython +Requires: python3-pandas +Requires: python3-requests +Requires: python3-scipy +Requires: python3-openpyxl +Requires: python3-tqdm + +%description +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png" + > +</p> +Now alpha support for prokaryotes too! + +<br /><br /> + +# NOTE +While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research. + +Cheers, +Zachary Konkel + +# PURPOSE +Bring broadscale comparative genomics to the masses. + +Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles. + +- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and + incomplete databases. +- `updateDB.py --update` brings the database to the current date. No more + database obsolecence in the wake of accelerating genome availability. +- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of + the `gff`, allowing for reliable analyses and format expectations from + multiple eras. +- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis. + +Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`. + +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png" + > +</p> + +<br /> + +By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`. + +<br /> + +# USAGE +Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide. + +<br /> + +# CITING +If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line. + +<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png"> + +<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> + + +%package -n python3-mycotools +Summary: A compilation of bioinformatic and computation biology inspired python tools +Provides: python-mycotools +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-mycotools +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png" + > +</p> +Now alpha support for prokaryotes too! + +<br /><br /> + +# NOTE +While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research. + +Cheers, +Zachary Konkel + +# PURPOSE +Bring broadscale comparative genomics to the masses. + +Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles. + +- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and + incomplete databases. +- `updateDB.py --update` brings the database to the current date. No more + database obsolecence in the wake of accelerating genome availability. +- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of + the `gff`, allowing for reliable analyses and format expectations from + multiple eras. +- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis. + +Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`. + +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png" + > +</p> + +<br /> + +By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`. + +<br /> + +# USAGE +Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide. + +<br /> + +# CITING +If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line. + +<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png"> + +<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> + + +%package help +Summary: Development documents and examples for mycotools +Provides: python3-mycotools-doc +%description help +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png" + > +</p> +Now alpha support for prokaryotes too! + +<br /><br /> + +# NOTE +While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research. + +Cheers, +Zachary Konkel + +# PURPOSE +Bring broadscale comparative genomics to the masses. + +Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles. + +- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and + incomplete databases. +- `updateDB.py --update` brings the database to the current date. No more + database obsolecence in the wake of accelerating genome availability. +- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of + the `gff`, allowing for reliable analyses and format expectations from + multiple eras. +- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis. + +Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`. + +<p align="center"> + <img + src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png" + > +</p> + +<br /> + +By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`. + +<br /> + +# USAGE +Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide. + +<br /> + +# CITING +If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line. + +<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png"> + +<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> + + +%prep +%autosetup -n mycotools-0.27.36 + +%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-mycotools -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.27.36-1 +- Package Spec generated |