Commit 0fdf3851 authored by Blaise Li's avatar Blaise Li

Merge branch 'master' of gitlab.pasteur.fr:bli/libhts

parents b8ad92ec 4eb4b3b8
#!/bin/sh
/usr/bin/env python3 setup.py build_ext
# .egg-link does not work with PYTHONPATH ?
# Install custom pybedtools first
/usr/bin/env python3 -m pip install -r requirements.txt
/usr/bin/env python3 -m pip install -e .
/usr/bin/env python3 -m pip install --no-deps --ignore-installed .
......@@ -5,6 +5,8 @@ networkx
numpy
pandas
pyBigWig
pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
# pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
pybedtools @ git+https://github.com/blaiseli/pybedtools.git@pep518
# pybedtools
scipy
seaborn
......@@ -26,7 +26,7 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# Requires:
# * bedops (for bedmap)
# * bedops (for bedmap) -> module load bedops/2.4.36
# * python3 -> module load Python/3.6.0
# * samtools -> module load samtools/1.9
# * bedtools -> module load bedtools/2.25.0
......@@ -34,6 +34,16 @@
# * parallel (for niceload) -> module load parallel/20170122
# * UCSC-tools (for bedGraphToBigWig) -> module load UCSC-tools/v373
load_tools ()
{
[ bedops --version 2> /dev/null ] || module load bedops/2.4.36
[ python3 -V 2> /dev/null ] || module load bedops/2.4.36
[ samtools --version 2> /dev/null ] || module load samtools/1.9
[ bedtools --version 2> /dev/null ] || module load bedtools/2.25.0
[ niceload --version 2> /dev/null ] || module load parallel/20170122
[ bedGraphToBigWig 2> /dev/null ] || module load UCSC-tools/v373
}
workdir=$(mktemp -d)
cleanup()
......@@ -58,6 +68,8 @@ error_exit ()
mawk --version 1> /dev/null 2> /dev/null || alias mawk='awk'
load_tools || error_exit "Some tools are not available"
bam=${1}
bin_file=${2}
# Example of how to generate the bin_file from iGenome data:
......@@ -66,6 +78,7 @@ bin_file=${2}
# | sed 's/SN://g' | sed 's/LN://' \
# | bedops --chop 10 - \
# > Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed
# A genome.dict file can be extracted from a bam file: samtools view -H <bam file>
# Ensure we use a 3 columns minimal bed for bin_file:
......
......@@ -42,7 +42,8 @@ setup(
"numpy",
"pandas",
"pyBigWig",
"pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
"pybedtools @ git+https://github.com/blaiseli/pybedtools.git@pep518",
# "pybedtools",
"scipy",
"seaborn"],
# specific versions and index would rather belong to requirements.txt
......
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