def install_biobambam(env):
version = "0.0.93"
revision = "20131002162026"
libmaus_version = "0.0.74"
libmaus_revision = "20131002161300"
url = "https://github.com/gt1/biobambam/archive/%s-release-%s.tar.gz" \
% (version, revision)
libmaus_url = "https://github.com/gt1/libmaus/archive/%s-release-%s.tar.gz" \
% (libmaus_version, libmaus_revision)
if not versioncheck.up_to_date(env, "bamtofastq --version", version, stdout_flag="This is biobambam version"):
if not versioncheck.up_to_date(env, "pkg-config --modversion libmaus", libmaus_version):
_get_install(libmaus_url, env, shared._configure_make)
_get_install(url, env, shared._configure_make)
def install_samtools(env):
"""SAM Tools provide various utilities for manipulating alignments in the SAM format.
http://samtools.sourceforge.net/
"""
default_version = "0.1.19"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env, "samtools", version, stdout_flag="Version:"):
env.logger.info("samtools version {0} is up to date; not installing"
.format(version))
return
url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
"%s/samtools-%s.tar.bz2" % (version, version)
def _safe_ncurses_make(env):
"""Combine samtools, removing ncurses refs if not present on system.
"""
with settings(warn_only=True):
result = env.safe_run("make")
# no ncurses, fix Makefile and rebuild
if result.failed:
env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
env.safe_sed("Makefile", "-lcurses", "# -lcurses")
env.safe_run("make clean")
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
for fname in env.safe_run_output("ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim").split("\n"):
env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
_get_install(url, env, _safe_ncurses_make)
def install_gemini(env):
"""A lightweight db framework for disease and population genetics.
https://github.com/arq5x/gemini
"""
version = "0.6.4"
if versioncheck.up_to_date(env, "gemini -v", version,
stdout_flag="gemini"):
return
elif not shared._executable_not_on_path("gemini -v"):
env.safe_run("gemini update")
else:
iurl = "https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py"
data_dir = os.path.join(
env.system_install,
"local" if env.system_install.find("/local") == -1 else "",
"share", "gemini")
with _make_tmp_dir(ext="-gemini") as work_dir:
with cd(work_dir):
if env.safe_exists(os.path.basename(iurl)):
env.safe_run("rm -f %s" % os.path.basename(iurl))
installer = shared._remote_fetch(env, iurl)
env.safe_run("%s %s %s %s %s" %
(_python_cmd(env), installer, "" if env.use_sudo
else "--nosudo", env.system_install, data_dir))
env.safe_run("rm -f gemini_install.py")
def install_samtools(env):
"""SAM Tools provide various utilities for manipulating alignments in the SAM format.
http://samtools.sourceforge.net/
"""
default_version = "0.1.19"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env,
"samtools",
version,
stdout_flag="Version:"):
env.logger.info(
"samtools version {0} is up to date; not installing".format(
version))
return
url = "http://downloads.sourceforge.net/project/samtools/samtools/" \
"%s/samtools-%s.tar.bz2" % (version, version)
def _safe_ncurses_make(env):
"""Combine samtools, removing ncurses refs if not present on system.
"""
with settings(warn_only=True):
result = env.safe_run("make")
# no ncurses, fix Makefile and rebuild
if result.failed:
env.safe_sed("Makefile", "-D_CURSES_LIB=1", "-D_CURSES_LIB=0")
env.safe_sed("Makefile", "-lcurses", "# -lcurses")
env.safe_run("make clean")
env.safe_run("make")
install_dir = shared._get_bin_dir(env)
for fname in env.safe_run_output(
"ls -1 samtools bcftools/bcftools bcftools/vcfutils.pl misc/wgsim"
).split("\n"):
env.safe_sudo("cp -f %s %s" % (fname.rstrip("\r"), install_dir))
_get_install(url, env, _safe_ncurses_make)
def install_freebayes(env):
"""Bayesian haplotype-based polymorphism discovery and genotyping.
https://github.com/ekg/freebayes
"""
version = "0.9.9.2-21"
revision = "4f2fe5eee"
if versioncheck.up_to_date(env,
"freebayes",
version,
stdout_flag="version:"):
return
repository = "git clone --recursive https://github.com/ekg/freebayes.git"
def _fix_tabixpp_library_order(env):
env.safe_sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
def _fix_autoversion(env):
env.safe_sed("src/Makefile",
"all: autoversion ../bin/freebayes ../bin/bamleftalign",
"all: ../bin/freebayes ../bin/bamleftalign")
def _freebayes_fixes(env):
_fix_tabixpp_library_order(env)
_fix_autoversion(env)
_get_install(repository,
env,
_make_copy("ls -1 bin/*"),
post_unpack_fn=_freebayes_fixes,
revision=revision)
def install_lumpy(env):
"""a general probabilistic framework for structural variant discovery
https://github.com/arq5x/lumpy-sv
"""
version = "0.1.2"
revision = "a8b9e14cc5"
if versioncheck.up_to_date(env, "lumpy", version, stdout_flag="Program:"):
return
repository = "git clone https://github.com/arq5x/lumpy-sv.git"
def _add_gsl_includes():
"""Add multi-environment include and library links for finding GNU Scientific Libraries.
"""
env.safe_sed("defs.local", "^\([^#]\)", "#\1")
env.safe_append(
"defs.local",
("GSL_INCLUDE=-I/usr/local/include -I/usr/local/include/gsl "
"-I/usr/include/gsl -I%s/include/gsl" % env.system_install))
env.safe_append("defs.local",
("GSL_LINK=-L/usr/local/lib -L/usr/lib -L%s/lib" %
env.system_install))
_get_install(repository,
env,
_make_copy("ls -1 bin/*", _add_gsl_includes),
revision=revision)
def install_biobambam(env):
version = "0.0.96"
revision = "20131022183655"
libmaus_version = "0.0.77"
libmaus_revision = "20131022183354"
url = "https://github.com/gt1/biobambam/archive/%s-release-%s.tar.gz" \
% (version, revision)
libmaus_url = "https://github.com/gt1/libmaus/archive/%s-release-%s.tar.gz" \
% (libmaus_version, libmaus_revision)
if not versioncheck.up_to_date(env,
"bamtofastq --version",
version,
stdout_flag="This is biobambam version"):
if not versioncheck.up_to_date(env, "pkg-config --modversion libmaus",
libmaus_version):
_get_install(libmaus_url, env, shared._configure_make)
_get_install(url, env, shared._configure_make)
def install_bedtools(env):
"""A flexible suite of utilities for comparing genomic features.
https://code.google.com/p/bedtools/
"""
version = "2.17.0"
if versioncheck.up_to_date(env, "bedtools --version", version, stdout_flag="bedtools"):
return
url = "https://bedtools.googlecode.com/files/" \
"BEDTools.v%s.tar.gz" % version
_get_install(url, env, _make_copy("ls -1 bin/*"))
def install_delly(env):
"""DELLY: Structural variant discovery by integrated paired-end and split-read analysis
http://www.embl.de/~rausch/delly.html
"""
version = "0.0.11"
if versioncheck.up_to_date(env, "delly", version, stdout_flag="Deletion finder"):
return
url = "http://www.embl.de/~rausch/delly_v%s.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f",
do_make=False))
def install_delly(env):
"""DELLY: Structural variant discovery by integrated paired-end and split-read analysis
http://www.embl.de/~rausch/delly.html
"""
version = "0.0.11"
if versioncheck.up_to_date(env, "delly", version, stdout_flag="Deletion finder"):
return
url = "http://www.embl.de/~rausch/delly_v%s.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f",
do_make=False))
def install_freec(env):
"""Control-FREEC: a tool for detection of copy number changes and allelic imbalances.
http://bioinfo-out.curie.fr/projects/freec/
"""
version = "6.4"
if env.distribution in ["ubuntu", "debian"]:
if env.is_64bit:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz"
else:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_LINUX32.tar.gz"
if not versioncheck.up_to_date(env, "freec", version, stdout_index=1):
_get_install(url, env, _make_copy("find -name 'freec'"), dir_name=".")
def install_freec(env):
"""Control-FREEC: a tool for detection of copy number changes and allelic imbalances.
http://bioinfo-out.curie.fr/projects/freec/
"""
version = "6.4"
if env.distribution in ["ubuntu", "debian"]:
if env.is_64bit:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz"
else:
url = "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_LINUX32.tar.gz"
if not versioncheck.up_to_date(env, "freec", version, stdout_index=1):
_get_install(url, env, _make_copy("find -name 'freec'"), dir_name=".")
def install_bedtools(env):
"""A flexible suite of utilities for comparing genomic features.
https://code.google.com/p/bedtools/
"""
version = "2.17.0"
if versioncheck.up_to_date(env,
"bedtools --version",
version,
stdout_flag="bedtools"):
return
url = "https://bedtools.googlecode.com/files/" \
"BEDTools.v%s.tar.gz" % version
_get_install(url, env, _make_copy("ls -1 bin/*"))
def install_featurecounts(env):
"""
featureCounts from the subread package for counting reads mapping to
genomic features
"""
default_version = "1.4.4"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env, "featureCounts", version, stdout_flag="Version"):
return
platform = "MacOS" if env.distribution == "macosx" else "Linux"
url = ("http://downloads.sourceforge.net/project/subread/"
"subread-%s/subread-%s-%s-x86_64.tar.gz"
% (version, version, platform))
_get_install(url, env, _make_copy("find . -type f -perm -100 -name 'featureCounts'",
do_make=False))
def install_grabix(env):
"""a wee tool for random access into BGZF files
https://github.com/arq5x/grabix
"""
version = "0.1.1"
try:
uptodate = versioncheck.up_to_date(env, "grabix", version, stdout_flag="version:")
# Old versions will not have any version information
except IOError:
uptodate = False
if uptodate:
return
revision = "80150d00e5"
repository = "git clone https://github.com/arq5x/grabix.git"
_get_install(repository, env, _make_copy("ls -1 grabix"),
revision=revision)
def install_vcftools(env):
"""Work with VCF files, such as those generated by the 1000 Genomes Project.
http://vcftools.sourceforge.net/
"""
version = "0.1.11"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
if versioncheck.up_to_date(env, "vcftools", version, stdout_flag="VCFtools"):
return
def _vcf_make(env):
env.safe_sudo("make install PREFIX={dir}".format(dir=env.system_install))
for perl_module in ["FaSlice.pm", "Vcf.pm", "VcfStats.pm"]:
env.safe_sudo("cp perl/%s %s/lib/perl5" % (perl_module, env.system_install))
env.safe_sudo("make clean")
_get_install(url, env, _vcf_make)
_get_install_local(url, env, _make_copy())
def install_vcftools(env):
"""Work with VCF files, such as those generated by the 1000 Genomes Project.
http://vcftools.sourceforge.net/
"""
version = "0.1.11"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
if versioncheck.up_to_date(env, "vcftools", version, stdout_flag="VCFtools"):
return
def _vcf_make(env):
env.safe_sudo("make install PREFIX={dir}".format(dir=env.system_install))
for perl_module in ["FaSlice.pm", "Vcf.pm", "VcfStats.pm"]:
env.safe_sudo("cp perl/%s %s/lib/perl5" % (perl_module, env.system_install))
env.safe_sudo("make clean")
_get_install(url, env, _vcf_make)
_get_install_local(url, env, _make_copy())
def install_bwa(env):
"""BWA: aligns short nucleotide sequences against a long reference sequence.
http://bio-bwa.sourceforge.net/
"""
default_version = "0.7.5a"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env, "bwa", version, stdout_flag="Version:"):
return
url = "http://downloads.sourceforge.net/project/bio-bwa/bwa-%s.tar.bz2" % (
version)
def _fix_makefile():
arch = env.safe_run_output("uname -m")
# if not 64bit, remove the appropriate flag
if arch.find("x86_64") == -1:
env.safe_run("sed -i.bak -r -e 's/-O2 -m64/-O2/g' Makefile")
_get_install(url, env, _make_copy("ls -1 bwa qualfa2fq.pl",
_fix_makefile))
def install_bwa(env):
"""BWA: aligns short nucleotide sequences against a long reference sequence.
http://bio-bwa.sourceforge.net/
"""
default_version = "0.7.5a"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env, "bwa", version, stdout_flag="Version:"):
return
url = "http://downloads.sourceforge.net/project/bio-bwa/bwa-%s.tar.bz2" % (
version)
def _fix_makefile():
arch = env.safe_run_output("uname -m")
# if not 64bit, remove the appropriate flag
if arch.find("x86_64") == -1:
env.safe_run("sed -i.bak -r -e 's/-O2 -m64/-O2/g' Makefile")
_get_install(url, env, _make_copy("ls -1 bwa qualfa2fq.pl",
_fix_makefile))
def install_lumpy(env):
"""a general probabilistic framework for structural variant discovery
https://github.com/arq5x/lumpy-sv
"""
version = "0.1.2"
revision = "a8b9e14cc5"
if versioncheck.up_to_date(env, "lumpy", version, stdout_flag="Program:"):
return
repository = "git clone https://github.com/arq5x/lumpy-sv.git"
def _add_gsl_includes():
"""Add multi-environment include and library links for finding GNU Scientific Libraries.
"""
env.safe_sed("defs.local", "^\([^#]\)", "#\1")
env.safe_append("defs.local", ("GSL_INCLUDE=-I/usr/local/include -I/usr/local/include/gsl "
"-I/usr/include/gsl -I%s/include/gsl" % env.system_install))
env.safe_append("defs.local", ("GSL_LINK=-L/usr/local/lib -L/usr/lib -L%s/lib" % env.system_install))
_get_install(repository, env, _make_copy("ls -1 bin/*", _add_gsl_includes),
revision=revision)
def install_freebayes(env):
"""Bayesian haplotype-based polymorphism discovery and genotyping.
https://github.com/ekg/freebayes
"""
version = "0.9.9.2-14"
revision = "10ac8d449"
if versioncheck.up_to_date(env, "freebayes", version, stdout_flag="version:"):
return
repository = "git clone --recursive https://github.com/ekg/freebayes.git"
def _fix_tabixpp_library_order(env):
env.safe_sed("vcflib/tabixpp/Makefile", "-ltabix", "-ltabix -lz")
def _fix_autoversion(env):
env.safe_sed("src/Makefile", "all: autoversion ../bin/freebayes ../bin/bamleftalign",
"all: ../bin/freebayes ../bin/bamleftalign")
def _freebayes_fixes(env):
_fix_tabixpp_library_order(env)
_fix_autoversion(env)
_get_install(repository, env, _make_copy("ls -1 bin/*"),
post_unpack_fn=_freebayes_fixes,
revision=revision)
def install_featurecounts(env):
"""
featureCounts from the subread package for counting reads mapping to
genomic features
"""
default_version = "1.4.4"
version = env.get("tool_version", default_version)
if versioncheck.up_to_date(env,
"featureCounts",
version,
stdout_flag="Version"):
return
platform = "MacOS" if env.distribution == "macosx" else "Linux"
url = ("http://downloads.sourceforge.net/project/subread/"
"subread-%s/subread-%s-%s-x86_64.tar.gz" %
(version, version, platform))
_get_install(
url, env,
_make_copy("find . -type f -perm -100 -name 'featureCounts'",
do_make=False))
def install_grabix(env):
"""a wee tool for random access into BGZF files
https://github.com/arq5x/grabix
"""
version = "0.1.2"
revision = "a78cbaf488"
try:
uptodate = versioncheck.up_to_date(env,
"grabix",
version,
stdout_flag="version:")
# Old versions will not have any version information
except IOError:
uptodate = False
if uptodate:
return
repository = "git clone https://github.com/arq5x/grabix.git"
_get_install(repository,
env,
_make_copy("ls -1 grabix"),
revision=revision)
def install_gemini(env):
"""A lightweight db framework for disease and population genetics.
https://github.com/arq5x/gemini
"""
version = "0.6.1"
if versioncheck.up_to_date(env, "gemini -v", version, stdout_flag="gemini"):
return
elif not shared._executable_not_on_path("gemini -v"):
env.safe_run("gemini update")
else:
iurl = "https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py"
data_dir = os.path.join(env.system_install,
"local" if env.system_install.find("/local") == -1 else "",
"share", "gemini")
with _make_tmp_dir(ext="-gemini") as work_dir:
with cd(work_dir):
if env.safe_exists(os.path.basename(iurl)):
env.safe_run("rm -f %s" % os.path.basename(iurl))
installer = shared._remote_fetch(env, iurl)
env.safe_run("%s %s %s %s %s" %
(_python_cmd(env), installer, "" if env.use_sudo else "--nosudo",
env.system_install, data_dir))
env.safe_run("rm -f gemini_install.py")