From 2930f769c35b9e8c547367f10f0e629fe725a4ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Tue, 17 Nov 2015 11:33:39 +0100 Subject: [PATCH 1/3] Fix bash as a terminal. --- smbl/include_all.snake | 21 +-------------------- smbl/prog/prog.snake | 25 ------------------------- 2 files changed, 1 insertion(+), 45 deletions(-) delete mode 100644 smbl/prog/prog.snake diff --git a/smbl/include_all.snake b/smbl/include_all.snake index 95533f7..3c04e60 100644 --- a/smbl/include_all.snake +++ b/smbl/include_all.snake @@ -1,29 +1,10 @@ import smbl from snakemake.utils import min_version -shell.prefix("set -e -o pipefail; ") +shell.executable("/bin/bash") -#include: "utils/rules.snake" -#include: "prog/prog.snake" include: "fasta/fasta.snake" -#rule smbl_clean: -# shell: -# 'rm -fR "{}" "{}" "{}"'.format(smbl.bin_dir,smbl.fa_dir,smbl.src_dir) -# -#rule smbl_clean_fa: -# shell: -# 'rm -fR "{}"'.format(smbl.fa_dir) -# -#rule smbl_clean_prog: -# shell: -# 'rm -fR "{}"'.format(smbl.bin_dir) -# -#rule smbl_clean_src: -# shell: -# 'rm -fR "{}"'.format(smbl.src_dir) - - for i, rule in enumerate(smbl.utils.get_registered_rules()): rule: input: diff --git a/smbl/prog/prog.snake b/smbl/prog/prog.snake deleted file mode 100644 index 2e3da0c..0000000 --- a/smbl/prog/prog.snake +++ /dev/null @@ -1,25 +0,0 @@ -import smbl - -#for i, plugin in enumerate(smbl.prog.plugins.get_registered_plugins()): -# rule: -# output: -# plugin.get_installation_files() -# input: -# [ -# p.get_installation_files() for p in plugin.depends_on() -# ] -# params: -# i=str(i), -# run: -# (smbl.prog.plugins.get_registered_plugins()[int(params.i)].install_all_steps)() - -#for i, rule in enumerate(smbl.prog.plugins.get_registered_rules()): -# rule: -# input: -# rule.get_input() -# output: -# rule.get_output() -# params: -# i=str(i), -# run: -# smbl.prog.plugins.get_registered_rules()[int(params.i)].run() From eb78d7be7d66a713af0bc12989d6c9be8b549824 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Tue, 17 Nov 2015 11:45:10 +0100 Subject: [PATCH 2/3] Multithreading tests instead of single thread. --- .travis.yml | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/.travis.yml b/.travis.yml index eedd99b..5c03d60 100644 --- a/.travis.yml +++ b/.travis.yml @@ -26,21 +26,9 @@ install: - sudo apt-get install git-svn # libraries for HDF5 - sudo apt-get install libhdf5-serial-dev -#libhdf5-openmpi-dev libhdf5-mpich-dev libhdf5-lam-dev - pip install -r requirements.txt - pip install . script: - tests/tests_examples.sh -- tests/tests_st.sh +- tests/tests_mt.sh #- tests/tests_fa.sh -deploy: - provider: pypi - user: karel.brinda - distributions: "sdist" - password: - secure: dG6t/kcAyEK+LZR2mzj5SywUOtpvaoFde3dUdNr5J/lEvp1crv8fTQS0iTVaVmO71H/SRtakXWqTzABDYIyB+RnDYVzfQOog8gb+hr2JLr2XPFEhRbbQ2VDoLH21TJTAbTXAoA/jCVcv0FjeL5pA7TCIZerUF0ZBYyGMSWc6hL8= - on: - repo: karel-brinda/smbl - branch: master - tags: true - From e019cd95507bfaf249686e0f92219c5f83f05a4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Tue, 17 Nov 2015 11:55:23 +0100 Subject: [PATCH 3/3] Better description in README. --- README.rst | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/README.rst b/README.rst index 4a9c7ae..a832ab8 100644 --- a/README.rst +++ b/README.rst @@ -1,13 +1,12 @@ SMBL - SnakeMake Bioinformatics Library ======================================= -.. image:: https://badges.gitter.im/Join%20Chat.svg - :alt: Join the chat at https://gitter.im/karel-brinda/smbl - :target: https://gitter.im/karel-brinda/smbl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge - .. image:: https://travis-ci.org/karel-brinda/smbl.svg?branch=master :target: https://travis-ci.org/karel-brinda/smbl +.. image:: https://travis-ci.org/karel-brinda/smbl.svg?branch=devel + :target: https://travis-ci.org/karel-brinda/smbl + In case of any problem, don't hesitate to contact me on karel.brinda@gmail.com. @@ -16,31 +15,40 @@ Short description ----------------- **SMBL** is a library of some useful rules and Python functions which can be used in Snakemake (https://bitbucket.org/johanneskoester/snakemake/) pipelines. It makes possible to automatically -download various bioinformatics programs like read mappers, read simulators, conversion tools, etc. +install various bioinformatics programs like read mappers, read simulators, conversion tools, etc. It supports also downloading and conversion of some important references in FASTA format (e.g., human genome). Installation / upgrade ---------------------- -To install SMBL, you need to have Unix-like operating system (e.g., Linux, MacOS) and Python at least 3.2. +To install SMBL, you need to have Unix-like operating system (e.g., Linux, MacOS) and Python at least 3.3. Installation / upgrade can be performed using the following command. .. code-block:: bash - pip install --upgrade smbl + pip3 install --upgrade smbl If SnakeMake has not been installed, yet, it will be installed automatically with SMBL. -The current GIT version of SMBL can be installed by +The current version of SMBL from git can be installed by .. code-block:: bash - git clone --depth 1 http://github.com/karel-brinda/smbl - cd smbl - ./install.sh + pip3 install --upgrade git+git://github.com/karel-brinda/smbl + + +Requirements +------------ + +To be able to download and install software automatically, SMBL requires the following programs to be present in you Unix system: + +* wget or curl +* gcc 4.7+ +* git +* make Usage @@ -182,8 +190,9 @@ FASTA files | Chimpanzee genome PANTR04 | ``smbl.fasta.CHIMP_PANTRO4`` | +------------------------------+------------------------------------------------------------+ + Example -~~~~~~~ +------- The following example demonstrates how SMBL can be used for automatic installation of software.