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pip).](#1-a-repo-that-contains-miscellaneous-pythonc-modulesprograms-a-standalone-python-module-palos-by-the-yfish-group-can-be-installed-by-pip)\n- [2 Prerequisites to run Python programs in Pymodule](#2-prerequisites-to-run-python-programs-in-pymodule)\n  - [2.1 PyPi package: Palos](#21-pypi-package-palos)\n  - [2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3](#211-package-future-fstrings-ensures-compatibility-between-python2-and-python3)\n  - [2.1.2 Build and upload the palos package to PyPi](#212-build-and-upload-the-palos-package-to-pypi)\n  - [2.2 Optional prerequisites](#22-optional-prerequisites)\n  - [2.3 Optional C++ libraries](#23-optional-c-libraries)\n- [3 Example on how to run some pymodule programs](#3-example-on-how-to-run-some-pymodule-programs)\n\nYu S. Huang, polyactis@gmail.com\n\n# 1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).\n\nThis repository is a mix of a python module 'palos' and other standalone programs developed and used by the yfish group, http://www.yfish.org/.\n\nIt contains code related to bioinformatics projects focusing on next-generation sequencing data, population genetics, genome-wide association studies, pedigree genetics, etc.\n\n[palos/](palos/) contains the source code of the [https://pypi.org/project/palos](https://pypi.org/project/palos) module. \n\n[palos/algorithm/](palos/algorithm/) contains pure algorithms, not specific to Bioinformatics.\n\n\n[GADA/](GADA/) contains a faster algorithm than the original GADA (2008/2009) by using a Red-Black tree. Now in an independent repo https://github.com/polyactis/eGADA.\n\n[ngs/](ngs/) contains programs analyzing next-generation sequencing data.\n\n# 2 Prerequisites to run Python programs in Pymodule\nMost programs in pymodule are dependent on the `palos` module, which is in [palos/](palos/). Installation of `palos` will trigger installation of other dependencies.\n\n## 2.1 PyPi package: Palos\nPalos supports Python3 primarily, but is ported to Python2 via https://github.com/asottile/future-fstrings because some pymodule programs are Python2-only.\n\nInstall/Upgrade the Python3 version of Palos\n```sh\npip3 install --upgrade palos\n```\n\n\nInstall/Upgrade the Python2 version of Palos\n```sh\n# to run some Python2 pymodule programs\npip install --upgrade palos\n```\n\n## 2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3\n\nPackage future-fstrings allows the use of f-string in Python2.\n```python\n# -*- coding: future_fstrings -*-\nthing = 'world'\nprint(f'hello {thing}')\n```\n\n## 2.1.2 Build and upload the palos package to PyPi\n\n```bash\n# Build the package.\n# sdist and bdist_wheel are both commands of setup.py, not package names.\npython3 setup.py sdist bdist_wheel\n\n# (Delete old ones beforehand) and Upload the compiled package file.\n# Enter your PyPi username (__token__) and password (!= the pypi.org account password).\ntwine upload dist/*\n\n```\n\n## 2.2 Optional prerequisites\n\nThe following pakcages are optional, only needed for some functions.\n\n1. mysqldb\n2. biopython\n3. pegaflow https://pypi.org/project/Pegaflow/\n4. psycopg2 http://initd.org/psycopg/\n5. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/\n6. python imaging library http://www.pythonware.com/products/pil/\n7. python-scientific http://www.scipy.org/\n8. biopython\n9. python-rpy2\n10. networkx https://networkx.lanl.gov/wiki\n11. hcluster\n12. python-h5py\n13. python-tables\n\n## 2.3 Optional C++ libraries\n\nRequired if you plan to compile all binaries in pymodule by typeing 'make all'.\n\napt-get install libhdf5-dev libhdf5-serial-dev libhdf5-cpp-100 hdf5-tools \\\n       libarmadillo-dev libboost-program-options-dev libboost-iostreams-dev \\\n       libboost-python-dev python-dev\n\n\n\n# 3 Example on how to run some pymodule programs\n\n```sh\n./ngs/DownsampleWorkflow.py  -h\n```\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolyactis%2Fpymodule","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpolyactis%2Fpymodule","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolyactis%2Fpymodule/lists"}