Mercurial > repos > alenail > chipsequtil_old

changeset 4:19d80c995d7b draft

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Deleted selected files
author alenail
date Mon, 28 Mar 2016 11:56:10 -0400
parents c62c2fd68a29
children b2a929e58437
files chipsequtil-master/._MANIFEST.in chipsequtil-master/._README.txt chipsequtil-master/._docs chipsequtil-master/._examples chipsequtil-master/._ez_setup.py chipsequtil-master/._install.sh chipsequtil-master/._org_settings.cfg chipsequtil-master/._org_settings.cfg.sample chipsequtil-master/._scripts chipsequtil-master/._setup.cfg chipsequtil-master/._setup.py chipsequtil-master/._src chipsequtil-master/._uninstall.py chipsequtil-master/.gitignore chipsequtil-master/MANIFEST.in chipsequtil-master/README.txt chipsequtil-master/ez_setup.py chipsequtil-master/install.sh chipsequtil-master/org_settings.cfg chipsequtil-master/org_settings.cfg.sample chipsequtil-master/setup.cfg chipsequtil-master/setup.py chipsequtil-master/uninstall.py
diffstat 23 files changed, 0 insertions(+), 616 deletions(-) [+]
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Binary file chipsequtil-master/._MANIFEST.in has changed
Binary file chipsequtil-master/._README.txt has changed
Binary file chipsequtil-master/._docs has changed
Binary file chipsequtil-master/._examples has changed
Binary file chipsequtil-master/._ez_setup.py has changed
Binary file chipsequtil-master/._install.sh has changed
Binary file chipsequtil-master/._org_settings.cfg has changed
Binary file chipsequtil-master/._org_settings.cfg.sample has changed
Binary file chipsequtil-master/._scripts has changed
Binary file chipsequtil-master/._setup.cfg has changed
Binary file chipsequtil-master/._setup.py has changed
Binary file chipsequtil-master/._src has changed
Binary file chipsequtil-master/._uninstall.py has changed
--- a/chipsequtil-master/.gitignore	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-*.swp
-build
-src/chipsequtil/org_settings.cfg
-dist
-*.pyc
--- a/chipsequtil-master/MANIFEST.in	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-include README.txt
-include org_settings.cfg.sample
-include setup.*
-recursive-include scripts *.py
-recursive-include src *.py
--- a/chipsequtil-master/README.txt	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-Installation
-============
-
-Before installing, make a copy of *org_settings.cfg.sample* to *org_settings.cfg* :
-
-  $> cp org_settings.cfg.sample org_settings.cfg
-
-In the new *org_settings.cfg*, create/edit the paths and categories desired for
-your system as appropriate.  When you have configured the file to your
-satisfaction, copy it into the root source directory:
-
-  $> cp org_settings.cfg src/chipsequtil/
-
-You can then install the package with:
-
-  $> python setup.py install
-
-
-If you'd like to install the package to a non-system directory (e.g., if you
-don't have permission to install system-wide packages), you can provide the
-*--prefix=PATH* argument to the install command:
-
-  $> python setup.py install --prefix=/path/to/dir
-
-Remember to add */path/to/dir* to your PYTHONPATH environment variable if it
-is not already there.  If you wish to add more system-wide paths/organisms to
-org_settings.cfg, either edit the file in the source directory as above and
-reinstall (good way) or edit the file in the directory where the package is
-installed (less good way).
--- a/chipsequtil-master/ez_setup.py	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,284 +0,0 @@
-#!python
-"""Bootstrap setuptools installation
-
-If you want to use setuptools in your package's setup.py, just include this
-file in the same directory with it, and add this to the top of your setup.py::
-
-    from ez_setup import use_setuptools
-    use_setuptools()
-
-If you want to require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, you can do so by supplying
-the appropriate options to ``use_setuptools()``.
-
-This file can also be run as a script to install or upgrade setuptools.
-"""
-import sys
-DEFAULT_VERSION = "0.6c11"
-DEFAULT_URL     = "http://pypi.python.org/packages/%s/s/setuptools/" % sys.version[:3]
-
-md5_data = {
-    'setuptools-0.6b1-py2.3.egg': '8822caf901250d848b996b7f25c6e6ca',
-    'setuptools-0.6b1-py2.4.egg': 'b79a8a403e4502fbb85ee3f1941735cb',
-    'setuptools-0.6b2-py2.3.egg': '5657759d8a6d8fc44070a9d07272d99b',
-    'setuptools-0.6b2-py2.4.egg': '4996a8d169d2be661fa32a6e52e4f82a',
-    'setuptools-0.6b3-py2.3.egg': 'bb31c0fc7399a63579975cad9f5a0618',
-    'setuptools-0.6b3-py2.4.egg': '38a8c6b3d6ecd22247f179f7da669fac',
-    'setuptools-0.6b4-py2.3.egg': '62045a24ed4e1ebc77fe039aa4e6f7e5',
-    'setuptools-0.6b4-py2.4.egg': '4cb2a185d228dacffb2d17f103b3b1c4',
-    'setuptools-0.6c1-py2.3.egg': 'b3f2b5539d65cb7f74ad79127f1a908c',
-    'setuptools-0.6c1-py2.4.egg': 'b45adeda0667d2d2ffe14009364f2a4b',
-    'setuptools-0.6c10-py2.3.egg': 'ce1e2ab5d3a0256456d9fc13800a7090',
-    'setuptools-0.6c10-py2.4.egg': '57d6d9d6e9b80772c59a53a8433a5dd4',
-    'setuptools-0.6c10-py2.5.egg': 'de46ac8b1c97c895572e5e8596aeb8c7',
-    'setuptools-0.6c10-py2.6.egg': '58ea40aef06da02ce641495523a0b7f5',
-    'setuptools-0.6c11-py2.3.egg': '2baeac6e13d414a9d28e7ba5b5a596de',
-    'setuptools-0.6c11-py2.4.egg': 'bd639f9b0eac4c42497034dec2ec0c2b',
-    'setuptools-0.6c11-py2.5.egg': '64c94f3bf7a72a13ec83e0b24f2749b2',
-    'setuptools-0.6c11-py2.6.egg': 'bfa92100bd772d5a213eedd356d64086',
-    'setuptools-0.6c2-py2.3.egg': 'f0064bf6aa2b7d0f3ba0b43f20817c27',
-    'setuptools-0.6c2-py2.4.egg': '616192eec35f47e8ea16cd6a122b7277',
-    'setuptools-0.6c3-py2.3.egg': 'f181fa125dfe85a259c9cd6f1d7b78fa',
-    'setuptools-0.6c3-py2.4.egg': 'e0ed74682c998bfb73bf803a50e7b71e',
-    'setuptools-0.6c3-py2.5.egg': 'abef16fdd61955514841c7c6bd98965e',
-    'setuptools-0.6c4-py2.3.egg': 'b0b9131acab32022bfac7f44c5d7971f',
-    'setuptools-0.6c4-py2.4.egg': '2a1f9656d4fbf3c97bf946c0a124e6e2',
-    'setuptools-0.6c4-py2.5.egg': '8f5a052e32cdb9c72bcf4b5526f28afc',
-    'setuptools-0.6c5-py2.3.egg': 'ee9fd80965da04f2f3e6b3576e9d8167',
-    'setuptools-0.6c5-py2.4.egg': 'afe2adf1c01701ee841761f5bcd8aa64',
-    'setuptools-0.6c5-py2.5.egg': 'a8d3f61494ccaa8714dfed37bccd3d5d',
-    'setuptools-0.6c6-py2.3.egg': '35686b78116a668847237b69d549ec20',
-    'setuptools-0.6c6-py2.4.egg': '3c56af57be3225019260a644430065ab',
-    'setuptools-0.6c6-py2.5.egg': 'b2f8a7520709a5b34f80946de5f02f53',
-    'setuptools-0.6c7-py2.3.egg': '209fdf9adc3a615e5115b725658e13e2',
-    'setuptools-0.6c7-py2.4.egg': '5a8f954807d46a0fb67cf1f26c55a82e',
-    'setuptools-0.6c7-py2.5.egg': '45d2ad28f9750e7434111fde831e8372',
-    'setuptools-0.6c8-py2.3.egg': '50759d29b349db8cfd807ba8303f1902',
-    'setuptools-0.6c8-py2.4.egg': 'cba38d74f7d483c06e9daa6070cce6de',
-    'setuptools-0.6c8-py2.5.egg': '1721747ee329dc150590a58b3e1ac95b',
-    'setuptools-0.6c9-py2.3.egg': 'a83c4020414807b496e4cfbe08507c03',
-    'setuptools-0.6c9-py2.4.egg': '260a2be2e5388d66bdaee06abec6342a',
-    'setuptools-0.6c9-py2.5.egg': 'fe67c3e5a17b12c0e7c541b7ea43a8e6',
-    'setuptools-0.6c9-py2.6.egg': 'ca37b1ff16fa2ede6e19383e7b59245a',
-}
-
-import sys, os
-try: from hashlib import md5
-except ImportError: from md5 import md5
-
-def _validate_md5(egg_name, data):
-    if egg_name in md5_data:
-        digest = md5(data).hexdigest()
-        if digest != md5_data[egg_name]:
-            print >>sys.stderr, (
-                "md5 validation of %s failed!  (Possible download problem?)"
-                % egg_name
-            )
-            sys.exit(2)
-    return data
-
-def use_setuptools(
-    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
-    download_delay=15
-):
-    """Automatically find/download setuptools and make it available on sys.path
-
-    `version` should be a valid setuptools version number that is available
-    as an egg for download under the `download_base` URL (which should end with
-    a '/').  `to_dir` is the directory where setuptools will be downloaded, if
-    it is not already available.  If `download_delay` is specified, it should
-    be the number of seconds that will be paused before initiating a download,
-    should one be required.  If an older version of setuptools is installed,
-    this routine will print a message to ``sys.stderr`` and raise SystemExit in
-    an attempt to abort the calling script.
-    """
-    was_imported = 'pkg_resources' in sys.modules or 'setuptools' in sys.modules
-    def do_download():
-        egg = download_setuptools(version, download_base, to_dir, download_delay)
-        sys.path.insert(0, egg)
-        import setuptools; setuptools.bootstrap_install_from = egg
-    try:
-        import pkg_resources
-    except ImportError:
-        return do_download()       
-    try:
-        pkg_resources.require("setuptools>="+version); return
-    except pkg_resources.VersionConflict, e:
-        if was_imported:
-            print >>sys.stderr, (
-            "The required version of setuptools (>=%s) is not available, and\n"
-            "can't be installed while this script is running. Please install\n"
-            " a more recent version first, using 'easy_install -U setuptools'."
-            "\n\n(Currently using %r)"
-            ) % (version, e.args[0])
-            sys.exit(2)
-        else:
-            del pkg_resources, sys.modules['pkg_resources']    # reload ok
-            return do_download()
-    except pkg_resources.DistributionNotFound:
-        return do_download()
-
-def download_setuptools(
-    version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir,
-    delay = 15
-):
-    """Download setuptools from a specified location and return its filename
-
-    `version` should be a valid setuptools version number that is available
-    as an egg for download under the `download_base` URL (which should end
-    with a '/'). `to_dir` is the directory where the egg will be downloaded.
-    `delay` is the number of seconds to pause before an actual download attempt.
-    """
-    import urllib2, shutil
-    egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3])
-    url = download_base + egg_name
-    saveto = os.path.join(to_dir, egg_name)
-    src = dst = None
-    if not os.path.exists(saveto):  # Avoid repeated downloads
-        try:
-            from distutils import log
-            if delay:
-                log.warn("""
----------------------------------------------------------------------------
-This script requires setuptools version %s to run (even to display
-help).  I will attempt to download it for you (from
-%s), but
-you may need to enable firewall access for this script first.
-I will start the download in %d seconds.
-
-(Note: if this machine does not have network access, please obtain the file
-
-   %s
-
-and place it in this directory before rerunning this script.)
----------------------------------------------------------------------------""",
-                    version, download_base, delay, url
-                ); from time import sleep; sleep(delay)
-            log.warn("Downloading %s", url)
-            src = urllib2.urlopen(url)
-            # Read/write all in one block, so we don't create a corrupt file
-            # if the download is interrupted.
-            data = _validate_md5(egg_name, src.read())
-            dst = open(saveto,"wb"); dst.write(data)
-        finally:
-            if src: src.close()
-            if dst: dst.close()
-    return os.path.realpath(saveto)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-def main(argv, version=DEFAULT_VERSION):
-    """Install or upgrade setuptools and EasyInstall"""
-    try:
-        import setuptools
-    except ImportError:
-        egg = None
-        try:
-            egg = download_setuptools(version, delay=0)
-            sys.path.insert(0,egg)
-            from setuptools.command.easy_install import main
-            return main(list(argv)+[egg])   # we're done here
-        finally:
-            if egg and os.path.exists(egg):
-                os.unlink(egg)
-    else:
-        if setuptools.__version__ == '0.0.1':
-            print >>sys.stderr, (
-            "You have an obsolete version of setuptools installed.  Please\n"
-            "remove it from your system entirely before rerunning this script."
-            )
-            sys.exit(2)
-
-    req = "setuptools>="+version
-    import pkg_resources
-    try:
-        pkg_resources.require(req)
-    except pkg_resources.VersionConflict:
-        try:
-            from setuptools.command.easy_install import main
-        except ImportError:
-            from easy_install import main
-        main(list(argv)+[download_setuptools(delay=0)])
-        sys.exit(0) # try to force an exit
-    else:
-        if argv:
-            from setuptools.command.easy_install import main
-            main(argv)
-        else:
-            print "Setuptools version",version,"or greater has been installed."
-            print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)'
-
-def update_md5(filenames):
-    """Update our built-in md5 registry"""
-
-    import re
-
-    for name in filenames:
-        base = os.path.basename(name)
-        f = open(name,'rb')
-        md5_data[base] = md5(f.read()).hexdigest()
-        f.close()
-
-    data = ["    %r: %r,\n" % it for it in md5_data.items()]
-    data.sort()
-    repl = "".join(data)
-
-    import inspect
-    srcfile = inspect.getsourcefile(sys.modules[__name__])
-    f = open(srcfile, 'rb'); src = f.read(); f.close()
-
-    match = re.search("\nmd5_data = {\n([^}]+)}", src)
-    if not match:
-        print >>sys.stderr, "Internal error!"
-        sys.exit(2)
-
-    src = src[:match.start(1)] + repl + src[match.end(1):]
-    f = open(srcfile,'w')
-    f.write(src)
-    f.close()
-
-
-if __name__=='__main__':
-    if len(sys.argv)>2 and sys.argv[1]=='--md5update':
-        update_md5(sys.argv[2:])
-    else:
-        main(sys.argv[1:])
-
-
-
-
-
-
--- a/chipsequtil-master/install.sh	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/bin/bash
-
-# this script installs chipsequtils into /usr/local on the cluster nodes
-# since the cluster nodes do not have root write access to the network
-# volumes from nodes other than node 9, sudo ... doesn't work with
-# setuptools because it writes egg_info to the source directory and I
-# can't figure out how to get it to write to a local directory.
-#
-# this script copies the entire chipsequtil source tree to /tmp on the
-# local machine, runs sudo ./setup.py install --prefix=/usr/local, and,
-# on success, deletes the temporary source directory
-#
-# it _must_ be run from the source directory
-
-TMPDIR="/tmp/chipsequtil_tmp_$(date +%F)"
-if [ ! -d $TMPDIR ]; then
-    echo "temporary source dir $TMPDIR does not exist, creating"
-    mkdir $TMPDIR
-fi
-
-cd ../
-echo "copying source tree to $TMPDIR"
-cp -vr -t $TMPDIR chipsequtil/{setup.*,ez_setup.py,src,scripts,setuptools*}
-cd $TMPDIR
-echo "cd'ed to $PWD, installing"
-sudo ./setup.py install --prefix=/usr/local
-if [ $? -eq 0 ]; then
-        echo "install successful, removing $TMPDIR"
-        cd
-        sudo rm -r $TMPDIR
-fi
--- a/chipsequtil-master/org_settings.cfg	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-# This file is used by org_settings.py to return sets of paths/settings like
-# genomic sequence files, genome sizes, etc.  It is formatted according to
-# Python's ConfigParser.CongifParser specification:
-#
-# http://docs.python.org/library/configparser.html
-#
-# Before installation, add any system-specific settings to the categories below,
-# where categories correspond to organism/genome names, creating new category
-# headings where desired.
-#
-# User-specific organisms and settings may be specified in:
-#
-#   os.path.expanduser('~/.org_settings.cfg')
-#
-# with the same format.  Settings in user configuration files override system-wide
-# settings.
-#
-# A minimal organism configuration requires at least genome_dir and genome_size,
-# other settings may be required for different tools (e.g. theme_* for THEME.py)
-#
-# field values can contain no spaces if they are to be exported to the command line
-# (i.e. with org_settings.py)
-
-[hg18]
-description=UCSC hg18 (March '06 build) with full TRANSFAC hypothesis set
-genome=hg18
-genome_dir=/nfs/genomes/human_gp_mar_06
-genome_size=2700000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-hg18-2010-08-17.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-hg18-2010-08-17.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
-theme_markov=%(genome_dir)s/hg18_promoters_3000_1000.markov
-
-[hg18clust]
-description=UCSC hg18 (March '06 build) with clustered TRANSFAC hypothesis set
-genome=hg18
-genome=hg18
-genome_dir=/nfs/genomes/human_gp_mar_06
-genome_size=2700000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-hg18-2010-08-17.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-hg18-2010-08-17.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-hg18-2010-08-17.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
-theme_markov=%(genome_dir)s/hg18_promoters_3000_1000.markov
-weeder_freqfiles_path=%(genome_dir)s/weeder
-
-[hg19]
-description=UCSC hg19 (Feb '09 build) with full TRANSFAC hypothesis set
-genome=hg19
-genome_dir=/nfs/genomes/human_gp_feb_09
-genome_size=2700000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s-2011-01-04.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s-2011-01-04.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
-theme_markov=%(genome_dir)s/hg19_promoters_3000_1000.markov
-
-[hg19clust]
-description=UCSC hg19 (Feb '09 build) with clustered TRANSFAC hypothesis set
-genome=hg19
-genome_dir=/nfs/genomes/human_gp_feb_09
-genome_size=2700000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s-2011-01-04.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s-2011-01-04.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s-2011-01-04.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
-theme_markov=%(genome_dir)s/hg19_promoters_3000_1000.markov
-
-[mm9]
-description=UCSC mm9 (July '07 build) with full TRANSFAC hypothesis set
-genome=mm9
-genome_dir=/nfs/genomes/mouse_gp_jul_07
-genome_size=2107000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s.txt
-affy_to_known_path=%(genome_dir)s/anno/knownToMOE43-%(genome)s.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
-theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
-
-[mm9clust]
-description=UCSC mm9 (July '07 build) with clustered TRANSFAC hypothesis set
-genome=mm9
-genome_dir=/nfs/genomes/mouse_gp_jul_07
-genome_size=2107000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-annotation_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
-refgene_anno_path=%(genome_dir)s/anno/refFlat-%(genome)s.txt
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-%(genome)s.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-%(genome)s.txt
-affy_to_known_path=%(genome_dir)s/anno/knownToMOE430-%(genome)s.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9_sym_clus4.tamo
-theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
-
-[mm8]
-description=UCSC mm8 (March '07 build) with full TRANSFAC hypothesis set
-genome=mm8
-genome_dir=/nfs/genomes/mouse_gp_mar_06
-genome_size=2107000000
-ucsc_chrom_sizes=%(genome_dir)s/%(genome)s.chrom.sizes
-refgene_anno_path=%(genome_dir)s/anno/refFlat-2010-08-26.txt
-annotation_path=%(refgene_anno_path)s
-known_gene_anno_path=%(genome_dir)s/anno/knownGene-2010-08-26.txt
-known_gene_xref_path=%(genome_dir)s/anno/kgXref-2010-08-26.txt
-affy_to_known_path=%(genome_dir)s/anno/knownToMOE430-2010-08-26.txt
-theme_hypotheses=/nfs/vendata/cwng/TRANSFAC/2010_transfac_vert_all_filtic9.tamo
-theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
-
-# others...
--- a/chipsequtil-master/org_settings.cfg.sample	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-# This file is used by org_settings.py to return sets of paths/settings like
-# genomic sequence files, genome sizes, etc.  It is formatted according to
-# Python's ConfigParser.CongifParser specification:
-#
-# http://docs.python.org/library/configparser.html
-#
-# Before installation, add any system-specific settings to the categories below,
-# where categories correspond to organism/genome names, creating new category
-# headings where desired.
-#
-# User-specific organisms and settings may be specified in:
-#
-#   os.path.expanduser('~/.org_settings.cfg')
-#
-# with the same format.  Settings in user configuration files override system-wide
-# settings.
-#
-# A minimal organism configuration requires at least genome_dir and genome_size,
-# other settings may be required for different tools (e.g. theme_* for THEME.py)
-#
-# field values can contain no spaces if they are to be exported to the command line
-# (i.e. with org_settings.py)
-
-[human]
-description=
-genome_dir=
-genome_size=
-annotation_path=
-theme_hyp=
-theme_markov=
-# others...
-
-[mouse]
-genome_dir=/nfs/genomes/mouse_gp_jul_07
-genome_size=2107000000
-annotation_path=%(genome_dir)s/anno/refFlat.txt
-theme_hyp=/nfs/vendata/cwng/motifs/TRANSFAC_vert_filt9_clus4_trunc.tamo
-theme_markov=/nfs/data/cwng/chipseq/hypotheses/Mouse.markov
-# others...
--- a/chipsequtil-master/setup.cfg	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-[install]
-prefix=~/arch/univ
--- a/chipsequtil-master/setup.py	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-
-from distutils.core import setup
-#from ez_setup import use_setuptools
-#use_setuptools()
-#from setuptools import setup
-
-# convenience is king
-opj = os.path.join
-
-# make sure org_settings.cfg is in source directory
-org_settings_fn = 'org_settings.cfg'
-dist_settings_path = opj(os.getcwd(),'src','chipsequtil',org_settings_fn)
-if not os.path.exists(dist_settings_path) :
-    sys.stderr.write('WARNING: %s could not be found \
-                      in distribution root directory.  org_settings.py script may \
-                      not work properly.\n'%dist_settings_path)
-
-scripts = ['scripts/build_chipseq_infosite.py',
-           'scripts/chipseq_pipeline.py',
-           'scripts/combine_gerald_stats.py',
-           'scripts/compare_microarray_binding.py',
-           'scripts/create_pipeline_script.py',
-           'scripts/extract_promoters.py',
-           'scripts/filter_bed_by_position_count.py',
-           'scripts/filter_macs_peaks.py',
-           'scripts/filter_gps_peaks.py',
-           'scripts/filter_mapped_known_genes.py',
-           'scripts/generate_stats_doc.py',
-           'scripts/gerald_stats.py',
-           'scripts/gerald_to_bed.py',
-           'scripts/integrate_macs_ucsc.py',
-           'scripts/join_mapped_known_genes.py',
-           'scripts/map_intervals.py',
-           'scripts/map_peaks_to_genes.py',
-           'scripts/map_peaks_to_known_genes.py',
-           'scripts/motif_scan.py',
-           'scripts/nibFrag.py',
-           'scripts/org_settings.py',
-           'scripts/peaks_to_fasta.py',
-           'scripts/plot_pos_vs_neg_peaks.py',
-           'scripts/plot_peak_loc_dist.py',
-           'scripts/probeset_to_known_gene.py',
-           'scripts/rejection_sample_fasta.py',
-           'scripts/sort_bed.py',
-           'scripts/split_file.py',
-           'scripts/split_qsub.py',
-           'scripts/THEME.sh',
-           'scripts/wait_for_qsub.py',
-           'scripts/wait_for_jobid.py',
-           'scripts/wqsub.py',
-           'scripts/wqsub_drmaa.py',
-           ]
-
-# setup and install
-setup(name='chipsequtil',
-      version='0.5',
-      author='Adam Labadorf',
-      author_email='alabadorf@gmail.com',
-      package_dir={'':'src'},
-      py_modules=['chipsequtil.nib','chipsequtil.util','chipsequtil.plotting',
-                  'chipsequtil.sampling','chipsequtil.seq'],
-      packages=['chipsequtil'],
-      package_data={'': ['org_settings.cfg']},
-      scripts=scripts,
-      #cmdclass={'uninstall': uninstall},
-     )
--- a/chipsequtil-master/uninstall.py	Mon Mar 28 11:55:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#TODO this doesn't work yet - consider doing this later, use the install 
-# -f|--force option for now
-
-# distutils doesn't handle uninstalling things, this class deletes all the files
-# this package installs if it has appropriate permissions to do it, otherwise
-# print out the files that must be deleted to uninstall
-class uninstall(build_py) :
-  def run(self) :
-
-
-    # delete modules
-    print self.distribution.py_modules
-
-    # delete extensions
-    print self.distribution.ext_modules
-
-    # delete packages
-    print self.distribution.packages
-
-    # delete package data
-    print self.distribution.package_data
-
-    # delete scripts
-    print self.distribution.scripts
-
-    print self.distribution.get_command_obj('install').get_outputs()
-
-  def remove_path(self,path) :
-    '''Attempt to remove the specified path, returning non-zero status code on error'''
-
-