Python Modules Available

The Fred Hutch python modules have the suffix -fh1. The -fh1 module is specific to the Hutch, and contains libraries that have been requested by Hutch users.

Available Python Bundles

Biopython/1.74-foss-2016b-Python-3.7.4

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

CITE/seq-Count-1.4.2-foss-2016b-Python-3.7.4

A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.

h5py/2.9.0-foss-2016b-Python-3.7.4

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

jupyter/1.0.0-foss-2016b-Python-3.7.4

JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data.

Keras/2.3.0-foss-2016b-Python-3.7.4

Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.

matplotlib/3.1.1-foss-2016b-Python-3.7.4

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

megalodon/1.0.0-alpha.1-foss-2016b-Python-3.7.4

Megalodon provides “basecalling augmentation” for raw nanopore sequencing reads, including direct, reference-guided SNP and modified base calling.

pkgconfig/1.3.1-foss-2016b-Python-3.7.4

pkgconfig is a Python module to interface with the pkg-config command line tool

pybedtools/0.8.0-foss-2016b-Python-3.7.4

pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.

pybind11/2.3.0-foss-2016b-Python-3.7.4

pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.

Pysam/0.15.3-foss-2016b-Python-3.7.4

Pysam is a python module for reading and manipulating Samfiles. It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

Pysamstats/1.1.2-foss-2016b-Python-3.7.4

A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file.

python/fire-0.2.1-foss-2016b-Python-3.7.4

Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

PyYAML/5.1.2-foss-2016b-Python-3.7.4

PyYAML is a YAML parser and emitter for the Python programming language.

scikit/learn-0.21.2-foss-2016b-Python-3.7.4

Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.

SWIG/4.0.0-foss-2016b-Python-3.7.4

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

TensorFlow/1.14.0-foss-2016b-Python-3.7.4

An open-source software library for Machine Intelligence

Theano/1.0.4-foss-2016b-Python-3.7.4

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

TraCeR/0.6.0-foss-2016b-Python-3.7.4

TraCeR reconstructs the sequences of rearranged and expressed T cell receptor genes from single-cell RNA-seq data. It then uses the TCR sequences to identify cells that have the same receptor sequences and so derive from the same original clonally-expanded cell.

Available Python Modules

fhPython-3.9.6-foss-2021b

Package List APScheduler-3.9.1 In-process task scheduler with Cron-like capabilities Automat-20.2.0 Self-service finite-state machines for the programme...

Python-3.6.6-foss-2016b-fh1

Known Issues None Package List APScheduler-3.6.0 In-process task scheduler with Cron-like capabilities AnyQt-0.0.10 PyQt4/PyQt5 compatibility l...

Python-3.6.7-foss-2016b-fh2

Package List APScheduler-3.5.3 In-process task scheduler with Cron-like capabilities AnyQt-0.0.10 PyQt4/PyQt5 compatibility layer. Babel-2.6.0 Interna...

Python-3.6.7-foss-2016b-fh1

Package List APScheduler-3.5.3 In-process task scheduler with Cron-like capabilities AnyQt-0.0.10 PyQt4/PyQt5 compatibility layer. Babel-2.6.0 Interna...

Python-3.6.7-foss-2018b

Package List Cython-0.29.1 The Cython compiler for writing C extensions for the Python language. PyNaCl-1.3.0 Python binding to the Networking and Crypt...

Python-3.6.5-foss-2016b-fh3

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.5.3 Internat...

Python-2.7.15-foss-2016b

Package List Cython-0.28.3 The Cython compiler for writing C extensions for the Python language. PyNaCl-1.2.1 Python binding to the Networking and Crypt...

Python-3.6.5-foss-2016b-fh2

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.5.3 Internat...

Python-3.6.2-foss-2016b-fh2

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.4.0 Internat...

Python-2.7.15-foss-2016b-fh1

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities Babel-2.5.3 Internationalization utilities BreaKmer 0.0.7 CNVki...

Python-3.6.5-foss-2016b-fh1

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.5.3 Internat...

Python-2.7.14-foss-2016b

Package List Cython-0.27.3 The Cython compiler for writing C extensions for the Python language. bitstring-3.1.5 Simple construction, analysis and modif...

Python-3.6.4-foss-2016b-fh2

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities Babel-2.5.3 Internationalization utilities CacheControl-0.12.4 ht...

Python-3.6.4-foss-2016b-fh3

Package List APScheduler-3.5.1 In-process task scheduler with Cron-like capabilities Babel-2.5.3 Internationalization utilities CacheControl-0.12.4 ht...

Python-2.7.14-foss-2016b-fh1

Package List APScheduler-3.4.0 In-process task scheduler with Cron-like capabilities Babel-2.5.1 Internationalization utilities BreaKmer 0.0.7 CNVki...

Python-3.6.4-foss-2016b-fh1

Package List APScheduler-3.5.0 In-process task scheduler with Cron-like capabilities Babel-2.5.1 Internationalization utilities CacheControl-0.12.3 ht...

Python-3.6.1-foss-2016b-fh3

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.4.0 Internat...

Python-2.7.12-foss-2016b

Package List Cython-0.24 The Cython compiler for writing C extensions for the Python language. arff-2.1.0 Python package for reading and writing Weka ar...

Python-3.6.3-foss-2016b-fh1

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities AnyQt-0.0.8 PyQt4/PyQt5 compatibility layer. Babel-2.5.1 Internat...

Python-3.6.1-foss-2016b-fh2

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.4.0 Internationalization utilities CacheControl-0.12.2 ht...

Python-3.6.1-foss-2016b-fh1

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.4.0 Internationalization utilities CacheControl-0.12.2 ht...

Python-3.6.0-foss-2016b

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities CacheControl-0.11.7 ht...

Python-3.5.2-foss-2016b-fh2

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cython-0.25.1 The Cyth...

Python-3.5.2-foss-2016b-fh1

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cython-0.23.4 The Cyth...

Python-3.5.1-foss-2015b-fh

Package List Cython-0.23.2 The Cython compiler for writing C extensions for the Python language. arff-2.1.0 Python package for reading and writing Weka ...

Python-2.7.9-intel-2015b-fh

Package List Cython-0.21.2 The Cython compiler for writing C extensions for the Python language. arff-2.0.1 Python package for reading and writing Weka ...

Python-2.7.9-goolf-1.7.20-fh

Package List Cython-0.21.2 The Cython compiler for writing C extensions for the Python language. arff-2.0.1 Python package for reading and writing Weka ...

Python-2.7.9-foss-2015b

Package List Cython-0.21.2 The Cython compiler for writing C extensions for the Python language. arff-2.0.1 Python package for reading and writing Weka ...

Python-2.7.13-foss-2016b

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities ConfigArgParse-0.11.0 ...

Python-2.7.13-foss-2016b-fh2

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.4.0 Internationalization utilities BreaKmer 0.0.7 CNVki...

Python-2.7.13-foss-2016b-fh1

Package List APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities Babel-2.4.0 Internationalization utilities CNVkit-0.8.5 Copy numb...

Python-2.7.12-foss-2016b-fh3

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities ConfigArgParse-0.11.0 ...

Python-2.7.12-foss-2016b-fh2

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities ConfigArgParse-0.11.0 ...

Python-2.7.12-foss-2016b-fh1

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cython-0.23.4 The Cyth...

Python-2.7.12-foss-2016a-fh2

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cython-0.23.4 The Cyth...

Python-2.7.12-foss-2016a-fh1

Package List APScheduler-3.2.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cython-0.23.4 The Cyth...

Python-2.7.11-foss-2016b-libX11-1.6.3

Package List Cython-0.23.4 The Cython compiler for writing C extensions for the Python language. arff-2.1.0 Python package for reading and writing Weka ...

Python-2.7.11-foss-2016a-libX11-1.6.3

Package List Cython-0.23.4 The Cython compiler for writing C extensions for the Python language. arff-2.1.0 Python package for reading and writing Weka ...

Python-2.7.11-foss-2016a-fh1

Package List APScheduler-3.1.0 In-process task scheduler with Cron-like capabilities Babel-2.3.4 Internationalization utilities Cycler-0.10.0 Composab...

Python-2.7.10-intel-2015b

Package List Cython-0.22 The Cython compiler for writing C extensions for the Python language. arff-2.0.2 Python package for reading and writing Weka ar...

Python-2.7.10-foss-2015b

Package List Cython-0.22 The Cython compiler for writing C extensions for the Python language. arff-2.0.2 Python package for reading and writing Weka ar...