def install_cortex_var(env):
"""De novo genome assembly and variation analysis from sequence data.
http://cortexassembler.sourceforge.net/index_cortex_var.html
"""
version = "1.0.5.20"
url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
"latest/CORTEX_release_v{0}.tgz".format(version)
def _cortex_build(env):
env.safe_sed("Makefile", "\-L/full/path/\S*",
"-L{0}/lib -L/usr/lib -L/usr/local/lib".format(env.system_install))
env.safe_sed("Makefile", "^IDIR_GSL =.*$",
"IDIR_GSL={0}/include -I/usr/include -I/usr/local/include".format(env.system_install))
env.safe_sed("Makefile", "^IDIR_GSL_ALSO =.*$",
"IDIR_GSL_ALSO={0}/include/gsl -I/usr/include/gsl -I/usr/local/include/gsl".format(
env.system_install))
with cd("libs/gsl-1.15"):
env.safe_run("make clean")
with cd("libs/htslib"):
env.safe_run("make clean")
env.safe_run("make")
for cols in ["1", "2", "3", "4", "5"]:
for kmer in ["31", "63", "95"]:
env.safe_run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
with cd("scripts/analyse_variants/needleman_wunsch"):
env.safe_sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
# Fix incompatibilities with gzfile struct in zlib 1.2.6+
for fix_gz in ["libs/string_buffer/string_buffer.c", "libs/bioinf/bioinf.c",
"libs/string_buffer/string_buffer.h", "libs/bioinf/bioinf.h"]:
env.safe_sed(fix_gz, "gzFile \*", "gzFile ")
env.safe_sed(fix_gz, "gzFile\*", "gzFile")
env.safe_run("make")
_get_install_local(url, env, _cortex_build)
def install_echo(env):
"""ECHO: A reference-free short-read error correction algorithm
http://uc-echo.sourceforge.net/
"""
version = "1_11"
url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" "echo_v{0}.tgz".format(version)
_get_install_local(url, env, _make_copy())
def install_stampy(env):
base_version = "1.0.15"
revision = "1360"
version = "{0}r{1}".format(base_version, revision)
url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" \
"stampy-{0}.tgz".format(version)
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.sourceforge.net/
"""
version = "r2012-05-18"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" "trinityrnaseq_%s.tar.gz" % version
_get_install_local(url, env, _make_copy())
def install_transabyss(env):
version = "1.2.0"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" "releases/%s/trans-ABySS-v%s.tar.gz" % (
version,
version,
)
_get_install_local(url, env, _make_copy(do_make=False))
def install_cortex_var(env):
"""De novo genome assembly and variation analysis from sequence data.
http://cortexassembler.sourceforge.net/index_cortex_var.html
"""
version = "1.0.5.20"
url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
"latest/CORTEX_release_v{0}.tgz".format(version)
def _cortex_build(env):
env.safe_sed("Makefile", "\-L/full/path/\S*",
"-L{0}/lib -L/usr/lib -L/usr/local/lib".format(env.system_install))
env.safe_sed("Makefile", "^IDIR_GSL =.*$",
"IDIR_GSL={0}/include -I/usr/include -I/usr/local/include".format(env.system_install))
env.safe_sed("Makefile", "^IDIR_GSL_ALSO =.*$",
"IDIR_GSL_ALSO={0}/include/gsl -I/usr/include/gsl -I/usr/local/include/gsl".format(
env.system_install))
with cd("libs/gsl-1.15"):
env.safe_run("make clean")
with cd("libs/htslib"):
env.safe_run("make clean")
env.safe_run("make")
for cols in ["1", "2", "3", "4", "5"]:
for kmer in ["31", "63", "95"]:
env.safe_run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
with cd("scripts/analyse_variants/needleman_wunsch"):
env.safe_sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
# Fix incompatibilities with gzfile struct in zlib 1.2.6+
for fix_gz in ["libs/string_buffer/string_buffer.c", "libs/bioinf/bioinf.c",
"libs/string_buffer/string_buffer.h", "libs/bioinf/bioinf.h"]:
env.safe_sed(fix_gz, "gzFile \*", "gzFile ")
env.safe_sed(fix_gz, "gzFile\*", "gzFile")
env.safe_run("make")
_get_install_local(url, env, _cortex_build)
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.sourceforge.net/
"""
version = "r2012-05-18"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq_%s.tar.gz" % version
_get_install_local(url, env, _make_copy())
def install_echo(env):
"""ECHO: A reference-free short-read error correction algorithm
http://uc-echo.sourceforge.net/
"""
version = "1_12"
url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" \
"echo_v{0}.tgz".format(version)
_get_install_local(url, env, _make_copy())
def install_transabyss(env):
"""Analyze ABySS multi-k-assembled shotgun transcriptome data.
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
"""
version = "1.4.4"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" \
"releases/%s/trans-ABySS-v%s.tar.gz" % (version, version)
_get_install_local(url, env, _make_copy(do_make=False))
def install_transabyss(env):
"""Analyze ABySS multi-k-assembled shotgun transcriptome data.
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
"""
version = "1.4.4"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" \
"releases/%s/trans-ABySS-v%s.tar.gz" % (version, version)
_get_install_local(url, env, _make_copy(do_make=False))
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.github.io/
"""
version = "2.0.2"
url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/" \
"v%s.tar.gz" % version
dir_name = "trinityrnaseq-%s" % version
_get_install_local(url, env, _make_copy(), dir_name=dir_name)
def install_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
base_version = "1.0.15"
revision = "1360"
version = "{0}r{1}".format(base_version, revision)
url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" "stampy-{0}.tgz".format(version)
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))
def install_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
base_version = "1.0.18"
revision = "1526"
version = "{0}r{1}".format(base_version, revision)
url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" \
"stampy-{0}.tgz".format(version)
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.github.io/
"""
version = "2.3.2"
url = "https://github.com/trinityrnaseq/trinityrnaseq/archive/" \
"Trinity-v%s.tar.gz" % version
dir_name = "trinityrnaseq-%s" % version
_get_install_local(url, env, _make_copy(),
dir_name=dir_name)
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.sourceforge.net/
"""
version = "r2012-10-05"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq_%s.tgz" % version
def _remove_werror(env):
env.safe_sed("trinity-plugins/jellyfish/Makefile.in", " -Werror", "")
_get_install_local(url, env, _make_copy(),
post_unpack_fn=_remove_werror)
def install_trinity(env):
"""Efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
http://trinityrnaseq.sourceforge.net/
"""
version = "r2012-10-05"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq_%s.tgz" % version
def _remove_werror(env):
env.safe_sed("trinity-plugins/jellyfish/Makefile.in", " -Werror", "")
_get_install_local(url, env, _make_copy(),
post_unpack_fn=_remove_werror)
def install_vep(env):
"""Variant Effects Predictor (VEP) from Ensembl.
http://ensembl.org/info/docs/variation/vep/index.html
"""
version = "branch-ensembl-74"
url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
"variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
"&pathrev={0}".format(version)
def _vep_install(env):
env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl -a a")
_get_install_local(url, env, _vep_install)
def install_vep(env):
"""Variant Effects Predictor (VEP) from Ensembl.
http://ensembl.org/info/docs/variation/vep/index.html
"""
version = "branch-ensembl-74"
url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
"variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
"&pathrev={0}".format(version)
def _vep_install(env):
env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl -a a")
_get_install_local(url, env, _vep_install)
def install_vcftools(env):
"""Work with VCF files, such as those generated by the 1000 Genomes Project.
http://vcftools.sourceforge.net/
"""
version = "0.1.9"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
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_vep(env):
"""Variant Effects Predictor (VEP) from Ensembl.
http://ensembl.org/info/docs/variation/vep/index.html
"""
version = "branch-ensembl-69"
url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
"variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
"&pathrev={0}".format(version)
cache_dbs = "24"
def _vep_install(env):
env.safe_sed("INSTALL.pl", 'my \$ok = <>', 'my $ok = "y"')
env.safe_sed("INSTALL.pl", ", <>\)", ', "{0}")'.format(cache_dbs))
env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl")
_get_install_local(url, env, _vep_install)
def install_vep(env):
"""Variant Effects Predictor (VEP) from Ensembl.
http://ensembl.org/info/docs/variation/vep/index.html
"""
version = "branch-ensembl-69"
url = "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/" \
"variant_effect_predictor.tar.gz?view=tar&root=ensembl" \
"&pathrev={0}".format(version)
cache_dbs = "24"
def _vep_install(env):
env.safe_sed("INSTALL.pl", 'my \$ok = <>', 'my $ok = "y"')
env.safe_sed("INSTALL.pl", ", <>\)", ', "{0}")'.format(cache_dbs))
env.safe_run("export FTP_PASSIVE=1 && perl INSTALL.pl")
_get_install_local(url, env, _vep_install)
def install_vcftools(env):
"""Work with VCF files, such as those generated by the 1000 Genomes Project.
http://vcftools.sourceforge.net/
"""
version = "0.1.9"
url = "http://downloads.sourceforge.net/project/vcftools/vcftools_{v}.tar.gz".format(
v=version)
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_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
version = "1.0.21"
# version = base_version
# revision = "1654"
# version = "{0}r{1}".format(base_version, revision)
# url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
# "stampy-%s.tgz" % (version)
# Ugh -- Stampy now uses a 'Stampy-latest' download target
url = "http://www.well.ox.ac.uk/bioinformatics/Software/" "Stampy-latest.tgz"
def _clean_makefile(env):
sed("makefile", " -Wl", "")
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(version), post_unpack_fn=_clean_makefile)
def install_stampy(env):
"""Stampy: mapping of short reads from illumina sequencing machines onto a reference genome.
http://www.well.ox.ac.uk/project-stampy
"""
version = "1.0.21"
#version = base_version
#revision = "1654"
#version = "{0}r{1}".format(base_version, revision)
#url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
# "stampy-%s.tgz" % (version)
# Ugh -- Stampy now uses a 'Stampy-latest' download target
url = "http://www.well.ox.ac.uk/bioinformatics/Software/" \
"Stampy-latest.tgz"
def _clean_makefile(env):
env.safe_sed("makefile", " -Wl", "")
_get_install_local(url, env, _make_copy(),
dir_name="stampy-{0}".format(version),
post_unpack_fn=_clean_makefile)
def install_cortex_var(env):
"""De novo genome assembly and variation analysis from sequence data.
http://cortexassembler.sourceforge.net/index_cortex_var.html
"""
version = "1.0.5.11"
url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
"latest/CORTEX_release_v{0}.tgz".format(version)
def _cortex_build(env):
sed("Makefile", "\-L/full/path/\S*", "-L{0}/lib".format(env.system_install))
sed("Makefile", "^IDIR_GSL=.*$", "IDIR_GSL={0}/include".format(env.system_install))
sed("Makefile", "^IDIR_GSL_ALSO=.*$", "IDIR_GSL_ALSO={0}/include/gsl".format(env.system_install))
for cols in ["1", "2", "3", "4", "5"]:
for kmer in ["31", "63", "95"]:
run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
with cd("scripts/analyse_variants/needleman_wunsch-0.3.0"):
sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
run("make")
_get_install_local(url, env, _cortex_build)
def install_cortex_var(env):
"""De novo genome assembly and variation analysis from sequence data.
http://cortexassembler.sourceforge.net/index_cortex_var.html
"""
version = "1.0.5.11"
url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
"latest/CORTEX_release_v{0}.tgz".format(version)
def _cortex_build(env):
sed("Makefile", "\-L/full/path/\S*", "-L{0}/lib".format(env.system_install))
sed("Makefile", "^IDIR_GSL=.*$", "IDIR_GSL={0}/include".format(env.system_install))
sed("Makefile", "^IDIR_GSL_ALSO=.*$", "IDIR_GSL_ALSO={0}/include/gsl".format(env.system_install))
for cols in ["1", "2", "3", "4", "5"]:
for kmer in ["31", "63", "95"]:
run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
with cd("scripts/analyse_variants/needleman_wunsch-0.3.0"):
sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
run("make")
_get_install_local(url, env, _cortex_build)
def install_stampy(env):
base_version = "1.0.15"
revision = "1360"
version = "{0}r{1}".format(base_version, revision)
url = "http://www.well.ox.ac.uk/~gerton/software/Stampy/" "stampy-{0}.tgz".format(version)
_get_install_local(url, env, _make_copy(), dir_name="stampy-{0}".format(base_version))
def install_trinity(env):
version = "03122011"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq-%s.tgz" % version
_get_install_local(url, env, _make_copy())
def install_transabyss(env):
version = "1.2.0"
url = "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/" \
"releases/%s/trans-ABySS-v%s.tar.gz" % (version, version)
_get_install_local(url, env, _make_copy(do_make=False))
def install_trinity(env):
version = "03122011"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" \
"trinityrnaseq-%s.tgz" % version
_get_install_local(url, env, _make_copy())
def install_echo(env):
version = "1_11"
url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" "echo_v{0}.tgz".format(version)
_get_install_local(url, env, _make_copy())
def install_echo(env):
version = "1_11"
url = "http://downloads.sourceforge.net/project/uc-echo/source%20release/" \
"echo_v{0}.tgz".format(version)
_get_install_local(url, env, _make_copy())
def install_trinity(env):
version = "r2012-05-18"
url = "http://downloads.sourceforge.net/project/trinityrnaseq/" "trinityrnaseq_%s.tar.gz" % version
_get_install_local(url, env, _make_copy())
