MANIFEST.in

#
# Use .add_data_files and .add_data_dir methods in a appropriate
# setup.py files to include non-python files such as documentation,
# data, etc files to distribution. Avoid using MANIFEST.in for that.
#
include MANIFEST.in
include LICENSE
include INSTALL
include README.rst
include KNOWN_BUGS
include THANKS.txt

include install-CGAT-tools.sh
include requires.txt

exclude CGAT/tools/*

# CGAT scripts to include - these
# are named explicitely
include CGAT/tools/bam_vs_bam.py
include CGAT/tools/bam_vs_bed.py
include CGAT/tools/bam_vs_gtf.py
include CGAT/tools/bam2bam.py
include CGAT/tools/bam2bed.py
include CGAT/tools/bam2fastq.py
include CGAT/tools/bam2geneprofile.py
include CGAT/tools/bam2peakshape.py
include CGAT/tools/bam2stats.py
include CGAT/tools/bam2wiggle.py
include CGAT/tools/bed2bed.py
include CGAT/tools/beds2counts.py
include CGAT/tools/bed2fasta.py
include CGAT/tools/bed2gff.py
include CGAT/tools/bed2stats.py
include CGAT/tools/bed2table.py
include CGAT/tools/beds2beds.py
include CGAT/tools/chain2psl.py
include CGAT/tools/chain2stats.py
include CGAT/tools/diff_bam.py
include CGAT/tools/diff_bed.py
include CGAT/tools/diff_chains.py
include CGAT/tools/diff_fasta.py
include CGAT/tools/diff_gtf.py
include CGAT/tools/fasta2bed.py
include CGAT/tools/fasta2fasta.py
include CGAT/tools/fasta2kmercontent.py
include CGAT/tools/fasta2table.py
include CGAT/tools/fasta2variants.py
include CGAT/tools/fastas2fasta.py
include CGAT/tools/fastq2fastq.py
include CGAT/tools/fastq2table.py
include CGAT/tools/fastqs2fasta.py
include CGAT/tools/fastqs2fastqs.py
include CGAT/tools/gff2bed.py
include CGAT/tools/gff2coverage.py
include CGAT/tools/gff2fasta.py
include CGAT/tools/gff2gff.py
include CGAT/tools/gff2histogram.py
include CGAT/tools/gff2psl.py
include CGAT/tools/gff2stats.py
include CGAT/tools/gtf2fasta.py
include CGAT/tools/gtf2gff.py
include CGAT/tools/gtf2gtf.py
include CGAT/tools/gtf2tsv.py
include CGAT/tools/gtf2table.py
include CGAT/tools/gtfs2tsv.py
include CGAT/tools/index_fasta.py
include CGAT/tools/randomize_lines.py
include CGAT/tools/split_gff.py
include CGAT/tools/vcf2vcf.py

# other CGAT/tools
include CGAT/tools/__init__.py
include CGAT/tools/cgat.py
include CGAT/tools/version.py

# extensions
# include CGAT/tools/*.pyxbld
# include CGAT/tools/*.pyx
include CGAT/Components/*.h
include CGAT/Components/*.cpp
include CGAT/NCL/*.h
include CGAT/NCL/*.pxd
include CGAT/NCL/intervaldb.c
include CGAT/Components/*.h
include CGAT/Components/*.cpp
include CGAT/BamTools/*.pyx
include CGAT/VCFTools/*.pyx