diff --git a/includes/setup.py b/includes/setup.py deleted file mode 100644 index d7557d4915180093e636dc8e422766b840558592..0000000000000000000000000000000000000000 --- a/includes/setup.py +++ /dev/null @@ -1,23 +0,0 @@ -from setuptools import setup, find_packages -#from Cython.Build import cythonize - -# Adapted from Biopython -__version__ = "Undefined" -for line in open('smincludes/__init__.py'): - if (line.startswith('__version__')): - exec(line.strip()) - -setup( - name="smincludes", - #version=libworkflows.__version__, - version=__version__, - description="Rules that can be included in snakemake workflows.", - author="Blaise Li", - author_email="blaise.li@normalesup.org", - license="MIT", - packages=find_packages(), - package_data={"smincludes": ["*.rules"]}, - ) - #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"), - #install_requires=["cytoolz"], - #zip_safe=False diff --git a/includes/install.sh b/install.sh similarity index 100% rename from includes/install.sh rename to install.sh diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..a260f9680126d456e9da08979bc640aaa3f312dc --- /dev/null +++ b/setup.py @@ -0,0 +1,14 @@ +from setuptools import setup, find_packages + +setup( + name="snakemake_wrappers", + version=0.2, + description="Snakemake wrappers and rules that can be included in snakemake workflows.", + author="Blaise Li", + author_email="blaise.li@normalesup.org", + license="MIT", + packages=find_packages(), + package_data={ + "smincludes": ["*.rules"], + "wrappers": ["*/wrapper.py"]}, + ) diff --git a/includes/smincludes/__init__.py b/smincludes/__init__.py similarity index 100% rename from includes/smincludes/__init__.py rename to smincludes/__init__.py diff --git a/includes/smincludes/link_raw_data.rules b/smincludes/link_raw_data.rules similarity index 100% rename from includes/smincludes/link_raw_data.rules rename to smincludes/link_raw_data.rules diff --git a/wrappers/__init__.py b/wrappers/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..276c01645b514d33d44ecdeec6e45c2f1a12081c --- /dev/null +++ b/wrappers/__init__.py @@ -0,0 +1,7 @@ +import os + +__all__ = ["wrappers_dir"] + +# The working directory is that of the importing context. +# __path__ gives access to the package path +wrappers_dir = __path__ diff --git a/bam2fastq/wrapper.py b/wrappers/bam2fastq/wrapper.py similarity index 100% rename from bam2fastq/wrapper.py rename to wrappers/bam2fastq/wrapper.py diff --git a/bigwig_average_over_bed/wrapper.py b/wrappers/bigwig_average_over_bed/wrapper.py similarity index 100% rename from bigwig_average_over_bed/wrapper.py rename to wrappers/bigwig_average_over_bed/wrapper.py diff --git a/compute_RPK/wrapper.py b/wrappers/compute_RPK/wrapper.py similarity index 100% rename from compute_RPK/wrapper.py rename to wrappers/compute_RPK/wrapper.py diff --git a/compute_TPM/wrapper.py b/wrappers/compute_TPM/wrapper.py similarity index 100% rename from compute_TPM/wrapper.py rename to wrappers/compute_TPM/wrapper.py diff --git a/feature_count_reads/wrapper.py b/wrappers/feature_count_reads/wrapper.py similarity index 100% rename from feature_count_reads/wrapper.py rename to wrappers/feature_count_reads/wrapper.py diff --git a/filter_size_bam/wrapper.py b/wrappers/filter_size_bam/wrapper.py similarity index 100% rename from filter_size_bam/wrapper.py rename to wrappers/filter_size_bam/wrapper.py diff --git a/filter_unique_bam/wrapper.py b/wrappers/filter_unique_bam/wrapper.py similarity index 100% rename from filter_unique_bam/wrapper.py rename to wrappers/filter_unique_bam/wrapper.py diff --git a/filter_unique_sam/wrapper.py b/wrappers/filter_unique_sam/wrapper.py similarity index 100% rename from filter_unique_sam/wrapper.py rename to wrappers/filter_unique_sam/wrapper.py diff --git a/htseq_count_reads/.snakemake.16u5vrtp.wrapper.py b/wrappers/htseq_count_reads/.snakemake.16u5vrtp.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.16u5vrtp.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.16u5vrtp.wrapper.py diff --git a/htseq_count_reads/.snakemake.5v24inro.wrapper.py b/wrappers/htseq_count_reads/.snakemake.5v24inro.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.5v24inro.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.5v24inro.wrapper.py diff --git a/htseq_count_reads/.snakemake.7d9py3f6.wrapper.py b/wrappers/htseq_count_reads/.snakemake.7d9py3f6.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.7d9py3f6.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.7d9py3f6.wrapper.py diff --git a/htseq_count_reads/.snakemake.by3fj1v8.wrapper.py b/wrappers/htseq_count_reads/.snakemake.by3fj1v8.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.by3fj1v8.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.by3fj1v8.wrapper.py diff --git a/htseq_count_reads/.snakemake.ftb48_zh.wrapper.py b/wrappers/htseq_count_reads/.snakemake.ftb48_zh.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.ftb48_zh.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.ftb48_zh.wrapper.py diff --git a/htseq_count_reads/.snakemake.km0dybww.wrapper.py b/wrappers/htseq_count_reads/.snakemake.km0dybww.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.km0dybww.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.km0dybww.wrapper.py diff --git a/htseq_count_reads/.snakemake.q4x91jrv.wrapper.py b/wrappers/htseq_count_reads/.snakemake.q4x91jrv.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.q4x91jrv.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.q4x91jrv.wrapper.py diff --git a/htseq_count_reads/.snakemake.q_427g9f.wrapper.py b/wrappers/htseq_count_reads/.snakemake.q_427g9f.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.q_427g9f.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.q_427g9f.wrapper.py diff --git a/htseq_count_reads/.snakemake.uh5y8lab.wrapper.py b/wrappers/htseq_count_reads/.snakemake.uh5y8lab.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.uh5y8lab.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.uh5y8lab.wrapper.py diff --git a/htseq_count_reads/.snakemake.v2tkj33z.wrapper.py b/wrappers/htseq_count_reads/.snakemake.v2tkj33z.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.v2tkj33z.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.v2tkj33z.wrapper.py diff --git a/htseq_count_reads/.snakemake.weqd46if.wrapper.py b/wrappers/htseq_count_reads/.snakemake.weqd46if.wrapper.py similarity index 100% rename from htseq_count_reads/.snakemake.weqd46if.wrapper.py rename to wrappers/htseq_count_reads/.snakemake.weqd46if.wrapper.py diff --git a/htseq_count_reads/wrapper.py b/wrappers/htseq_count_reads/wrapper.py similarity index 100% rename from htseq_count_reads/wrapper.py rename to wrappers/htseq_count_reads/wrapper.py diff --git a/intersect_count_reads/wrapper.py b/wrappers/intersect_count_reads/wrapper.py similarity index 100% rename from intersect_count_reads/wrapper.py rename to wrappers/intersect_count_reads/wrapper.py diff --git a/make_read_stats/wrapper.py b/wrappers/make_read_stats/wrapper.py similarity index 100% rename from make_read_stats/wrapper.py rename to wrappers/make_read_stats/wrapper.py diff --git a/map_on_genome/wrapper.py b/wrappers/map_on_genome/wrapper.py similarity index 100% rename from map_on_genome/wrapper.py rename to wrappers/map_on_genome/wrapper.py diff --git a/sam2indexedbam/wrapper.py b/wrappers/sam2indexedbam/wrapper.py similarity index 100% rename from sam2indexedbam/wrapper.py rename to wrappers/sam2indexedbam/wrapper.py