def main():
install_path = snakemake.config['paths']['install']+"/tools/"
raw_name="ngs_te_mapper-da9b7915b0b2fcd4daf70989d55755a03c3f73ea"
method_name = "ngs_te_mapper2"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url, snakemake.params.zipfile, md5=snakemake.params.md5, max_attempts=3)
if not download_success:
print(method_name+" download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install']+raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+raw_name)
command = ["mv", snakemake.config['paths']['install']+raw_name, install_path]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+method_name)
mccutils.mkdir(install_path+method_name)
for f in os.listdir(install_path+raw_name):
command = ["mv", install_path+raw_name+"/"+f, install_path+method_name]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+raw_name)
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install']+"/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url, snakemake.params.zipfile, md5=snakemake.params.md5, max_attempts=3)
if not download_success:
print("retroseq download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
extracted_file_name = "RetroSeq-9d4f3b5270af2383f40e6e7ea1204ea718365db2"
mccutils.remove(snakemake.config['paths']['install']+extracted_file_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+extracted_file_name)
command = ["mv", snakemake.config['paths']['install']+extracted_file_name, install_path]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+"retroseq")
mccutils.mkdir(install_path+"retroseq")
for f in os.listdir(install_path+extracted_file_name):
command = ["mv", install_path+extracted_file_name+"/"+f, install_path+"retroseq"]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+extracted_file_name)
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install']+"/tools/"
raw_name = "jitterbug-b6b3f9c7ee4af042d4410137269f174a1399b752"
mod_name = "jitterbug"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url, snakemake.params.zipfile, md5=snakemake.params.md5, max_attempts=3)
if not download_success:
print(mod_name+" download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install']+raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+raw_name)
command = ["mv", snakemake.config['paths']['install']+raw_name, install_path]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+mod_name)
mccutils.mkdir(install_path+mod_name)
for f in os.listdir(install_path+raw_name):
command = ["mv", install_path+raw_name+"/"+f, install_path+mod_name]
mccutils.run_command(command, log=snakemake.params.log)
command = ["patch", "-i", snakemake.params.patch, install_path+mod_name+"/jitterbug.py"]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path+raw_name)
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("teflon download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46")
command = [
"mv", snakemake.config['paths']['install'] +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "teflon")
mccutils.mkdir(install_path + "teflon")
for f in os.listdir(install_path +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46"):
command = [
"mv", install_path +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46/" + f,
install_path + "teflon"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.pseudo2refConvert_patch,
install_path + "teflon/teflon_scripts/pseudo2refConvert.py"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.teflon_patch,
install_path + "teflon/teflon.v0.4.py"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEFLoN-3e2d67886b70644fd1f7d79263b3c8dbed639e46")
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(
snakemake.config['paths']['install'] + "/tools/teflon/version.log",
"w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("popoolationte download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + "popoolationte")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "popoolationte")
mccutils.mkdir(install_path + "popoolationte")
for f in os.listdir(snakemake.config['paths']['install'] +
"popoolationte"):
command = [
"mv", snakemake.config['paths']['install'] + "popoolationte/" + f,
install_path + "popoolationte"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch1,
install_path + "popoolationte/Modules/TEInsertUtility.pm"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch2,
install_path + "popoolationte/Modules/TEInsert.pm"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch3,
install_path + "popoolationte/samro.pl"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch4,
install_path + "popoolationte/identify-te-insertsites.pl"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(snakemake.params.zipfile)
mccutils.remove(snakemake.config['paths']['install'] + "popoolationte")
# write version to file
with open(
snakemake.config['paths']['install'] +
"/tools/popoolationte/version.log", "w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("RelocaTE2 download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + "RelocaTE2-2.0.1")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "RelocaTE2-2.0.1")
command = [
"mv", snakemake.config['paths']['install'] + "RelocaTE2-2.0.1",
install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "relocate2")
mccutils.mkdir(install_path + "relocate2")
for f in os.listdir(install_path + "RelocaTE2-2.0.1"):
command = [
"mv", install_path + "RelocaTE2-2.0.1/" + f,
install_path + "relocate2"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "RelocaTE2-2.0.1")
mccutils.remove(snakemake.params.zipfile)
tools = [
"bwa", "bowtie2", "bowtie2_build", "blat", "samtools", "bedtools",
"seqtk"
]
with open(install_path + "relocate2/CONFIG", "w") as config_file:
config_file.write("#tools\n")
for tool in tools:
if tool == "bowtie2_build":
tool_bin = "bowtie2-build"
else:
tool_bin = tool
output = subprocess.Popen(["which", tool_bin],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
path = output.stdout.read()
path = path.decode()
line = tool + "=" + path
config_file.write(line)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("teflon download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c")
command = [
"mv", snakemake.config['paths']['install'] +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "teflon")
mccutils.mkdir(install_path + "teflon")
for f in os.listdir(install_path +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c"):
command = [
"mv", install_path +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c/" + f,
install_path + "teflon"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.pseudo2refConvert_patch,
install_path + "teflon/teflon_scripts/pseudo2refConvert.py"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.teflon_patch,
install_path + "teflon/teflon.v0.4.py"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEFLoN-9eca0152f3dd9dc6c44787a30d590f7e321b442c")
mccutils.remove(snakemake.params.zipfile)
def main():
download_success = mccutils.download(snakemake.params.url,
snakemake.output[0],
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("popoolationTE2 download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
# write version to file
with open(
snakemake.config['paths']['install'] +
"/tools/popoolationte2/version.log", "w") as version:
version.write(snakemake.params.md5)
def main():
script_dir = os.path.dirname(os.path.abspath(__file__))
# download fastq1
fq1 = script_dir+"/SRR800842_1.fastq.gz"
if os.path.exists(fq1):
print(fq1+" already exists...skipping...")
else:
download_success = mccutils.download(url['fq1'], fq1, md5=md5['fq1'], timeout=22000)
if not download_success:
print("Download of SRR800842_1.fastq.gz failed...please rerun script to try again")
mccutils.remove(fq1)
sys.exit(1)
# download fastq2
fq2 = script_dir+"/SRR800842_2.fastq.gz"
if os.path.exists(fq2):
print(fq2+" already exists...skipping...")
else:
download_success = mccutils.download(url['fq2'], fq2, md5=md5['fq2'], timeout=22000)
if not download_success:
print("Download of SRR800842_2.fastq.gz failed...please rerun script to try again")
mccutils.remove(fq2)
sys.exit(1)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("temp download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
extracted_file_name = "TEMP-4f67e1da836721a9f0999efa52e1e648fedb75fc"
mccutils.remove(snakemake.config['paths']['install'] + extracted_file_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + extracted_file_name)
command = [
"mv", snakemake.config['paths']['install'] + extracted_file_name,
install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "temp")
mccutils.mkdir(install_path + "temp")
for f in os.listdir(install_path + extracted_file_name):
command = [
"mv", install_path + extracted_file_name + "/" + f,
install_path + "temp"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch,
install_path + "temp/scripts/TEMP_Absence.sh"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + extracted_file_name)
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(snakemake.config['paths']['install'] + "/tools/temp/version.log",
"w") as version:
version.write(snakemake.params.md5)
def main():
mccutils.remove(snakemake.params.tar)
download_success = mccutils.download(snakemake.params.url, snakemake.params.tar, md5=snakemake.params.md5, max_attempts=3)
if not download_success:
print("TE-Locate download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
command = ["tar", "-xvf", snakemake.params.tar, "-C", snakemake.config['paths']['install']+"/tools/te-locate/"]
mccutils.run_command(command, log=snakemake.params.log)
# write version to file
with open(snakemake.config['paths']['install']+"/tools/te-locate/version.log","w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("temp download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1")
command = [
"mv", snakemake.config['paths']['install'] +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "temp")
mccutils.mkdir(install_path + "temp")
for f in os.listdir(install_path +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1"):
command = [
"mv", install_path +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1/" + f,
install_path + "temp"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch,
install_path + "temp/scripts/TEMP_Absence.sh"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"TEMP-d2500b904e2020d6a1075347b398525ede5feae1")
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
raw_name = "tebreak-3f00badda822dcb6390bbea5a6a1e233cff3e99c"
method_name = "tebreak"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print(method_name + " download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
command = [
"mv", snakemake.config['paths']['install'] + raw_name, install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + method_name)
mccutils.mkdir(install_path + method_name)
for f in os.listdir(install_path + raw_name):
command = [
"mv", install_path + raw_name + "/" + f, install_path + method_name
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(install_path + "/" + method_name + "/version.log",
"w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
raw_name = "ngs_te_mapper2-220619a3dd00b8c05c3b96328eb2424c6aad623e"
method_name = "ngs_te_mapper2"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print(method_name + " download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
command = [
"mv", snakemake.config['paths']['install'] + raw_name, install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + method_name)
mccutils.mkdir(install_path + method_name)
for f in os.listdir(install_path + raw_name):
command = [
"mv", install_path + raw_name + "/" + f, install_path + method_name
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(install_path + "/" + method_name + "/version.log",
"w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("ngs_te_mapper download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9")
command = [
"mv", snakemake.config['paths']['install'] +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "ngs_te_mapper")
mccutils.mkdir(install_path + "ngs_te_mapper")
for f in os.listdir(
install_path +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9"):
command = [
"mv", install_path +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9/" + f,
install_path + "ngs_te_mapper"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"ngs_te_mapper-fb23590200666fe66f1c417c5d5934385cb77ab9")
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
raw_name = "TEMP2-4d25d050dc7832b82374502573e882a242457a0c"
method_name = "temp2"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print(method_name + " download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
command = [
"mv", snakemake.config['paths']['install'] + raw_name, install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + method_name)
mccutils.mkdir(install_path + method_name)
for f in os.listdir(install_path + raw_name):
command = [
"mv", install_path + raw_name + "/" + f, install_path + method_name
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(install_path + "/" + method_name + "/version.log",
"w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
raw_name = "ngs_te_mapper-f9f48996ac346ac86d57edbd00534aa1227b753e"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("ngs_te_mapper download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] + raw_name)
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
command = [
"mv", snakemake.config['paths']['install'] + raw_name, install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "ngs_te_mapper")
mccutils.mkdir(install_path + "ngs_te_mapper")
for f in os.listdir(install_path + raw_name):
command = [
"mv", install_path + raw_name + "/" + f,
install_path + "ngs_te_mapper"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + raw_name)
mccutils.remove(snakemake.params.zipfile)
# write version to file
with open(install_path + "ngs_te_mapper/version.log", "w") as version:
version.write(snakemake.params.md5)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("retroseq download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0")
command = [
"mv", snakemake.config['paths']['install'] +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "retroseq")
mccutils.mkdir(install_path + "retroseq")
for f in os.listdir(install_path +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0"):
command = [
"mv", install_path +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0/" + f,
install_path + "retroseq"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"RetroSeq-700d4f76a3b996686652866f2b81fefc6f0241e0")
mccutils.remove(snakemake.params.zipfile)
def main():
install_path = snakemake.config['paths']['install'] + "/tools/"
mccutils.remove(snakemake.params.zipfile)
download_success = mccutils.download(snakemake.params.url,
snakemake.params.zipfile,
md5=snakemake.params.md5,
max_attempts=3)
if not download_success:
print("relocaTE download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)
mccutils.remove(snakemake.config['paths']['install'] +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b")
command = ["unzip", snakemake.params.zipfile]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b")
command = [
"mv", snakemake.config['paths']['install'] +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b", install_path
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path + "relocate")
mccutils.mkdir(install_path + "relocate/")
for f in os.listdir(install_path +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b"):
command = [
"mv", install_path +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b/" + f,
install_path + "relocate/"
]
mccutils.run_command(command, log=snakemake.params.log)
command = [
"patch", "-i", snakemake.params.patch,
install_path + "relocate/scripts/relocaTE_insertionFinder.pl"
]
mccutils.run_command(command, log=snakemake.params.log)
mccutils.remove(install_path +
"RelocaTE-ce3a2066e15f5c14e2887fdf8dce0485e1750e5b")
mccutils.remove(snakemake.params.zipfile)
output = subprocess.Popen(["which", "perl"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
perl_path = output.stdout.read()
perl_path = perl_path.decode()
for f in os.listdir(install_path + "relocate/scripts/"):
if "pl" == f.split(".")[-1]:
with open(install_path + "tmp", "w") as tmp:
with open(install_path + "relocate/scripts/" + f,
"r") as script:
for line in script:
if "#!/usr/bin/perl" in line:
# line = "#!"+perl_path
line = "#!/usr/bin/env perl\n"
elif "defined @" in line:
line = line.replace("defined @", "@")
elif "$scripts/" in line and "perl" not in line and "relocaTE.pl" in f:
line = line.replace("$scripts/", "perl $scripts/")
tmp.write(line)
mccutils.run_command([
"mv", install_path + "tmp",
install_path + "relocate/scripts/" + f
])
# write version to file
with open(
snakemake.config['paths']['install'] +
"/tools/relocate/version.log", "w") as version:
version.write(snakemake.params.md5)
def main():
download_success = mccutils.download(snakemake.params.url, snakemake.output[0], md5=snakemake.params.md5, max_attempts=3)
if not download_success:
print("popoolationTE2 download failed... exiting...")
print("try running --install with --clean for clean installation")
sys.exit(1)