From 6cae6f1f57e94c43b6aea6726454e98e35e57a63 Mon Sep 17 00:00:00 2001 From: Fabio Ticconi Date: Fri, 10 May 2019 17:23:15 +0200 Subject: [PATCH 1/3] fix setup --- python/setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/python/setup.py b/python/setup.py index a287250..f82249c 100755 --- a/python/setup.py +++ b/python/setup.py @@ -46,7 +46,7 @@ this_directory = path.abspath(path.dirname(__file__)) -with open(path.join(this_directory, 'readme.MD'), encoding='utf-8') as f: +with open(path.join(this_directory, 'readme.MD')) as f: long_description = f.read() setup (name = 'MOODS-python', @@ -61,6 +61,6 @@ ext_modules = [tools_mod, scan_mod, parsers_mod], packages = ["MOODS"], scripts=['scripts/moods-dna.py'], - classifiers=["Topic :: Scientific/Engineering :: Bio-Informatics"] + classifiers=["Topic :: Scientific/Engineering :: Bio-Informatics"], keywords="PWM, PSSM, motif scan" -) \ No newline at end of file +) From f0e5a3a5472ebfe780d8148eb1afdff8acf4d833 Mon Sep 17 00:00:00 2001 From: Fabio Ticconi Date: Fri, 10 May 2019 17:28:54 +0200 Subject: [PATCH 2/3] making the symlink for ease of compilation --- python/build.sh | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/python/build.sh b/python/build.sh index 678caff..6127af0 100755 --- a/python/build.sh +++ b/python/build.sh @@ -1,6 +1,11 @@ #!/bin/bash + +ln -sf ../core + swig -c++ -python -outdir MOODS/ core/scan.i swig -c++ -python -outdir MOODS/ core/tools.i swig -c++ -python -outdir MOODS/ core/misc.i swig -c++ -python -outdir MOODS/ core/parsers.i -python setup.py build_ext --inplace \ No newline at end of file + +python setup.py build_ext --inplace + From 408c8763f531ccbd2d3b6794977f2bacf36ba9ff Mon Sep 17 00:00:00 2001 From: Fabio Ticconi Date: Fri, 10 May 2019 18:03:21 +0200 Subject: [PATCH 3/3] minor fixes --- python/MANIFEST.in | 4 ++-- python/readme.MD | 8 ++++---- python/scripts/{moods_dna.py => moods-dna.py} | 0 3 files changed, 6 insertions(+), 6 deletions(-) rename python/scripts/{moods_dna.py => moods-dna.py} (100%) diff --git a/python/MANIFEST.in b/python/MANIFEST.in index a0bbf97..bb796c3 100644 --- a/python/MANIFEST.in +++ b/python/MANIFEST.in @@ -3,5 +3,5 @@ include readme.MD include scripts/example-data/readme.MD include scripts/example-data/seq/chr1-5k-55k.fa include scripts/example-data/matrices/* -include scripts/ex-*.py scripts/moods_dna.py -include COPYING.BIOPYTHON COPYING.GPLv3 \ No newline at end of file +include scripts/ex-*.py scripts/moods-dna.py +include COPYING.BIOPYTHON COPYING.GPLv3 diff --git a/python/readme.MD b/python/readme.MD index d94edde..198eb7b 100644 --- a/python/readme.MD +++ b/python/readme.MD @@ -32,7 +32,7 @@ Alternatively, you can install MOODS from the source package: (a) Compile the extensions in place and create a symlink under `scripts/` (if you just want to test things without installing to Python library path, -or you are simply planning to use the `moods_dna.py` scripts for basic +or you are simply planning to use the `moods-dna.py` scripts for basic analysis): python setup.py build_ext --inplace @@ -47,12 +47,12 @@ analysis): sudo python setup.py install -You can test MOODS by running the `moods_dna.py` script with +You can test MOODS by running the `moods-dna.py` script with the example data provided with the package: cd scripts/ - python moods_dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001 - python moods_dna.py --help + python moods-dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001 + python moods-dna.py --help Documentation diff --git a/python/scripts/moods_dna.py b/python/scripts/moods-dna.py similarity index 100% rename from python/scripts/moods_dna.py rename to python/scripts/moods-dna.py