Merge pull request #3 from dib-lab/clickify

initial clickification and packaging of genome-grist

.gitignore

@@ -4,3 +4,5 @@ outputs/
 *~
 test.db.sbt.json
 .sbt.test.db
+__pycache__
+.eggs

LICENSE.txt

@@ -0,0 +1,35 @@
+=======
+License
+=======
+
+Files: *
+Copyright: 2020, The Regents of the University of California.
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+
+     * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+     * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
+
+     * Neither the name of The Regents of the University of
+       California, nor the names of contributors may be used to
+       endorse or promote products derived from this software without
+       specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

conf.yml

@@ -0,0 +1 @@
+sample: SRR606249

genome_grist/__main__.py

@@ -0,0 +1,159 @@
+"Enable python -m genome_grist.click"
+import sys
+import os
+import subprocess
+
+import click
+
+
+def get_snakefile_path(name):
+    thisdir = os.path.dirname(__file__)
+    snakefile = os.path.join(thisdir, "conf", name)
+    return snakefile
+
+
+def get_package_configfile(filename):
+    thisdir = os.path.dirname(__file__)
+    configfile = os.path.join(thisdir, "conf", filename)
+    return configfile
+
+
+def run_snakemake(
+    configfile,
+    no_use_conda=False,
+    verbose=False,
+    snakefile_name="Snakefile",
+    outdir=None,
+    extra_args=[],
+):
+    # find the Snakefile relative to package path
+    snakefile = get_snakefile_path(snakefile_name)
+
+    # basic command
+    cmd = ["snakemake", "-s", snakefile]
+
+    # add --use-conda
+    if not no_use_conda:
+        cmd += ["--use-conda"]
+
+    # add --outdir
+    if outdir:
+        cmd += ["--config", f"outdir={outdir}"]
+
+    # snakemake sometimes seems to want a default -j; set it to 1 for now.
+    # can overridden later on command line.
+    cmd += ["-j", "1"]
+
+    # add rest of snakemake arguments
+    cmd += list(extra_args)
+
+    # add configfile - try looking for it a few different ways.
+    configfiles = []
+    if os.path.isfile(configfile):
+        configfiles = [configfile]
+    elif os.path.isfile(get_package_configfile(configfile)):
+        configfiles = [get_package_configfile(configfile)]
+    else:
+        for suffix in ".yaml", ".conf":
+            tryfile = configfile + suffix
+            if os.path.isfile(tryfile):
+                configfiles = [tryfile]
+                break
+
+            tryfile = get_package_configfile(tryfile)
+            if os.path.isfile(tryfile):
+                configfiles = [tryfile]
+                break
+
+    if not configfiles:
+        raise ValueError(f"cannot find config file '{configfile}'")
+
+    cmd += ["--configfile"] + configfiles
+
+    if verbose:
+        print("final command:", cmd)
+
+    # runme
+    try:
+        subprocess.check_call(cmd)
+    except subprocess.CalledProcessError as e:
+        print(f"Error in snakemake invocation: {e}", file=sys.stderr)
+        return e.returncode
+
+    return 0
+
+
+#
+# actual command line functions
+#
+
+
+@click.group()
+def cli():
+    pass
+
+
+# create a run subcommand that by default passes all of its arguments
+# on to snakemake (after setting Snakefile and config)
+@click.command(context_settings={"ignore_unknown_options": True})
+@click.argument("configfile")
+@click.option("--no-use-conda", is_flag=True, default=False)
+@click.option("--verbose", is_flag=True)
+@click.option("--outdir", nargs=1)
+@click.argument("snakemake_args", nargs=-1)
+def run(configfile, snakemake_args, no_use_conda, verbose, outdir):
+    "execute genome-grist workflow (using snakemake underneath)"
+    run_snakemake(
+        configfile,
+        snakefile_name="Snakefile",
+        no_use_conda=no_use_conda,
+        verbose=verbose,
+        extra_args=snakemake_args,
+        outdir=outdir,
+    )
+
+
+# 'check' command
+@click.command()
+@click.argument("configfile")
+def check(configfile):
+    "check configuration"
+    run_snakemake(configfile, extra_args=["check"])
+
+
+# 'showconf' command
+@click.command()
+@click.argument("configfile")
+def showconf(configfile):
+    "show full configuration"
+    run_snakemake(configfile, extra_args=["showconf"])
+
+
+# 'info' command
+@click.command()
+def info():
+    "provide basic install/config file info"
+    from .version import version
+
+    print(
+        f"""
+This is genome-grist version v{version}
+
+Package install path: {os.path.dirname(__file__)}
+snakemake Snakefile: {get_snakefile_path('Snakefile')}
+"""
+    )
+
+
+cli.add_command(run)
+cli.add_command(check)
+cli.add_command(showconf)
+cli.add_command(info)
+
+
+def main():
+    cli()
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -0,0 +1,45 @@
+from setuptools import setup, find_packages
+
+# read the contents of your README file
+from os import path
+this_directory = path.abspath(path.dirname(__file__))
+with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
+   long_description = f.read()
+
+CLASSIFIERS = [
+    "Environment :: Console",
+    "Environment :: MacOS X",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+setup(
+    name = 'genome-grist',
+    version = "0.1",
+    description="tools to support genome and metagenome analysis",
+    url="https://github.com/dib-lab/genome-grist",
+    author="C. Titus Brown, Luiz Irber, Tessa Pierce, Taylor Reiter",
+    author_email="[email protected],[email protected],[email protected],[email protected]",
+    license="BSD 3-clause",
+    packages = find_packages(),
+    classifiers = CLASSIFIERS,
+    entry_points = {'console_scripts': [
+        'genome-grist  = genome_grist.__main__:main'
+        ]
+    },
+    include_package_data=True,
+    package_data = { "genome_grist": ["Snakefile", "*.yml", "*.ipynb"] },
+    setup_requires = [ "setuptools>=38.6.0",
+                       'setuptools_scm', 'setuptools_scm_git_archive' ],
+    use_scm_version = {"write_to": "genome_grist/version.py"},
+    install_requires = ['snakemake>=5.10', 'click>=7'],
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+)

snakemake.slurm

@@ -0,0 +1,35 @@
+#!/bin/bash -login
+#SBATCH -p med2                # partition, or queue, to assign to
+#SBATCH -J gather-paper            # name for job
+#SBATCH -N 1                   # one "node", or computer
+#SBATCH -n 1                   # one task for this node
+#SBATCH -c 32                  # cores per task
+#SBATCH -t 2-0                 # ask for 2 days
+#SBATCH --mem=120000             # memory (30,000 mb = 30gb)
+#SBATCH --mail-type=ALL
+#SBATCH [email protected]
+
+# initialize conda
+. ~/miniconda3/etc/profile.d/conda.sh
+
+# activate your desired conda environment
+conda activate charcoal
+
+# fail on weird errors
+set -o nounset
+set -o errexit
+set -x
+
+# go to the directory you ran 'sbatch' in, OR just hardcode it...
+#cd $SLURM_SUBMIT_DIR
+cd ~/genome-grist
+
+# run the snakemake!
+python -m genome_grist run conf.yml -j 32 --use-conda -n
+
+# print out various information about the job
+env | grep SLURM            # Print out values of the current jobs SLURM environment variables
+
+scontrol show job ${SLURM_JOB_ID}     # Print out final statistics about resource uses before job exits
+
+sstat --format 'JobID,MaxRSS,AveCPU' -P ${SLURM_JOB_ID}.batch