URL = {
    "te-locate" : "https://downloads.sourceforge.net/project/te-locate/TE-locate.tar",
    "retroseq" : "https://github.com/tk2/RetroSeq/archive/9d4f3b5270af2383f40e6e7ea1204ea718365db2.zip",
    "temp" : "https://github.com/JialiUMassWengLab/TEMP/archive/4f67e1da836721a9f0999efa52e1e648fedb75fc.zip",
    "temp2": "https://github.com/weng-lab/TEMP2/archive/4d25d050dc7832b82374502573e882a242457a0c.zip",
    "relocate" : "https://github.com/srobb1/RelocaTE/archive/ce3a2066e15f5c14e2887fdf8dce0485e1750e5b.zip",
    "ngs_te_mapper" : "https://github.com/bergmanlab/ngs_te_mapper/archive/f9f48996ac346ac86d57edbd00534aa1227b753e.zip",
    "ngs_te_mapper2": "https://github.com/bergmanlab/ngs_te_mapper2/archive/220619a3dd00b8c05c3b96328eb2424c6aad623e.zip",
    "popoolationte" : "http://downloads.sourceforge.net/project/popoolationte/popoolationte_1.02.zip",
    "popoolationte2": "http://downloads.sourceforge.net/project/popoolation-te2/popte2-v1.10.03.jar",
    "relocate2" : "https://github.com/stajichlab/RelocaTE2/archive/v2.0.1.zip",
    "tepid" : "https://github.com/ListerLab/TEPID/archive/ad46d65b5c41bf8a9171215d49b3ffaecdceaab0.zip",
    "teflon": "https://github.com/jradrion/TEFLoN/archive/3e2d67886b70644fd1f7d79263b3c8dbed639e46.zip",
    "jitterbug": "https://github.com/elzbth/jitterbug/archive/b6b3f9c7ee4af042d4410137269f174a1399b752.zip",
    "tebreak": "https://github.com/adamewing/tebreak/archive/3f00badda822dcb6390bbea5a6a1e233cff3e99c.zip"
}

MD5 = {
    "te-locate" : "c28e3dd7be89a8efcfbca8939923787c",
    "retroseq" : "54030657dd8476f1a65f5f71e809b4c3",
    "temp" : "f06e25244e9979510a9743bcd9c841a5",
    "temp2" : "55b6449113e85540f8a39bb02cfec9b0",
    "relocate" : "64cc60f65154368518529fb57becc3d6",
    "ngs_te_mapper" : "a00e9962ee3daca9fac915c23c6af203",
    "ngs_te_mapper2": "95198ab68fcb4f9dc267460a7f906fae",
    "popoolationte" : "315d266bd6da7487c919576dc46b92b4",
    "popoolationte2": "0c06186f0b1df215949f57a5cbb2d039",
    "relocate2" : "63eb7dbc09ffeb4063aef4857d198b06",
    "tepid" : "51f61acf138b07842074f054aba780d5",
    "teflon" : "a29d2e7411fd06778186ba322f51fdc9",
    "jitterbug": "05f165fb6a79a7a611d09981a355d27e",
    "tebreak": "ac475d3cc4b0435f0a333c8d86f57d3f"
}

ENV_PATH = "{{envpath}}"
ENV = {
    "coverage" : ENV_PATH+"mcc_coverage.yml",
    "te-locate" : ENV_PATH+"mcc_telocate.yml",
    "retroseq" : ENV_PATH+"mcc_retroseq.yml",
    "temp" : ENV_PATH+"mcc_temp.yml",
    "temp2" : ENV_PATH+"mcc_temp2.yml",
    "relocate" : ENV_PATH+"mcc_relocate.yml",
    "ngs_te_mapper" : ENV_PATH+"mcc_ngs_te_mapper.yml",
    "ngs_te_mapper2": ENV_PATH+"mcc_ngs_te_mapper2.yml",
    "popoolationte" : ENV_PATH+"mcc_popoolationte.yml",
    "popoolationte2" : ENV_PATH+"mcc_popoolationte2.yml",
    "relocate2" : ENV_PATH+"mcc_relocate2.yml",
    "tepid" : ENV_PATH+"mcc_tepid.yml",
    "teflon" : ENV_PATH+"mcc_teflon.yml",
    "jitterbug": ENV_PATH+"mcc_jitterbug.yml",
    "setup_reads": ENV_PATH+"mcc_trimgalore.yml",
    "processing":  ENV_PATH+"mcc_map_reads.yml",
    "map_reads": ENV_PATH+"mcc_map_reads.yml",
    "trimgalore": ENV_PATH+"mcc_trimgalore.yml",
    "tebreak": ENV_PATH+"mcc_tebreak.yml"
}

INSTALL_PATH = "{{inspath}}"
OUTPUT = {
    "coverage" : INSTALL_PATH+"tools/coverage/coverage.log",
    "te-locate" : INSTALL_PATH+"tools/te-locate/TE_locate.pl",
    "retroseq" : INSTALL_PATH+"tools/retroseq/bin/retroseq.pl",
    "temp" : INSTALL_PATH+"tools/temp/scripts/TEMP_Insertion.sh",
    "temp2" : INSTALL_PATH+"tools/temp2/TEMP2",
    "relocate" : INSTALL_PATH+"tools/relocate/scripts/relocaTE_insertionFinder.pl",
    "ngs_te_mapper" : INSTALL_PATH+"tools/ngs_te_mapper/sourceCode/run_ngs_te_mapper.sh",
    "ngs_te_mapper2": INSTALL_PATH+"tools/ngs_te_mapper2/sourceCode/ngs_te_mapper2.py",
    "popoolationte" : INSTALL_PATH+"tools/popoolationte/identify-te-insertsites.pl",
    "popoolationte2" : INSTALL_PATH+"tools/popoolationte2/popte2-v1.10.03.jar",
    "relocate2" : INSTALL_PATH+"tools/relocate2/scripts/relocaTE2.py",
    "tepid" : INSTALL_PATH+"tools/tepid/tepid-map",
    "teflon" : INSTALL_PATH+"tools/teflon/teflon.v0.4.py",
    "jitterbug": INSTALL_PATH+"tools/jitterbug/jitterbug.py",
    "map_reads" : INSTALL_PATH+"tools/map_reads/map_reads.log",
    "trimgalore" : INSTALL_PATH+"tools/trimgalore/trimgalore.log",
    "tebreak" : INSTALL_PATH+"tools/tebreak/tebreak/tebreak"
}

bbbca7461c9379f7ef565099c932005172925884
<mask token>

URL = {'te-locate':
    'https://downloads.sourceforge.net/project/te-locate/TE-locate.tar',
    'retroseq':
    'https://github.com/tk2/RetroSeq/archive/9d4f3b5270af2383f40e6e7ea1204ea718365db2.zip'
    , 'temp':
    'https://github.com/JialiUMassWengLab/TEMP/archive/4f67e1da836721a9f0999efa52e1e648fedb75fc.zip'
    , 'temp2':
    'https://github.com/weng-lab/TEMP2/archive/4d25d050dc7832b82374502573e882a242457a0c.zip'
    , 'relocate':
    'https://github.com/srobb1/RelocaTE/archive/ce3a2066e15f5c14e2887fdf8dce0485e1750e5b.zip'
    , 'ngs_te_mapper':
    'https://github.com/bergmanlab/ngs_te_mapper/archive/f9f48996ac346ac86d57edbd00534aa1227b753e.zip'
    , 'ngs_te_mapper2':
    'https://github.com/bergmanlab/ngs_te_mapper2/archive/220619a3dd00b8c05c3b96328eb2424c6aad623e.zip'
    , 'popoolationte':
    'http://downloads.sourceforge.net/project/popoolationte/popoolationte_1.02.zip'
    , 'popoolationte2':
    'http://downloads.sourceforge.net/project/popoolation-te2/popte2-v1.10.03.jar'
    , 'relocate2':
    'https://github.com/stajichlab/RelocaTE2/archive/v2.0.1.zip', 'tepid':
    'https://github.com/ListerLab/TEPID/archive/ad46d65b5c41bf8a9171215d49b3ffaecdceaab0.zip'
    , 'teflon':
    'https://github.com/jradrion/TEFLoN/archive/3e2d67886b70644fd1f7d79263b3c8dbed639e46.zip'
    , 'jitterbug':
    'https://github.com/elzbth/jitterbug/archive/b6b3f9c7ee4af042d4410137269f174a1399b752.zip'
    , 'tebreak':
    'https://github.com/adamewing/tebreak/archive/3f00badda822dcb6390bbea5a6a1e233cff3e99c.zip'
    }
MD5 = {'te-locate': 'c28e3dd7be89a8efcfbca8939923787c', 'retroseq':
    '54030657dd8476f1a65f5f71e809b4c3', 'temp':
    'f06e25244e9979510a9743bcd9c841a5', 'temp2':
    '55b6449113e85540f8a39bb02cfec9b0', 'relocate':
    '64cc60f65154368518529fb57becc3d6', 'ngs_te_mapper':
    'a00e9962ee3daca9fac915c23c6af203', 'ngs_te_mapper2':
    '95198ab68fcb4f9dc267460a7f906fae', 'popoolationte':
    '315d266bd6da7487c919576dc46b92b4', 'popoolationte2':
    '0c06186f0b1df215949f57a5cbb2d039', 'relocate2':
    '63eb7dbc09ffeb4063aef4857d198b06', 'tepid':
    '51f61acf138b07842074f054aba780d5', 'teflon':
    'a29d2e7411fd06778186ba322f51fdc9', 'jitterbug':
    '05f165fb6a79a7a611d09981a355d27e', 'tebreak':
    'ac475d3cc4b0435f0a333c8d86f57d3f'}
ENV_PATH = '{{envpath}}'
ENV = {'coverage': ENV_PATH + 'mcc_coverage.yml', 'te-locate': ENV_PATH +
    'mcc_telocate.yml', 'retroseq': ENV_PATH + 'mcc_retroseq.yml', 'temp': 
    ENV_PATH + 'mcc_temp.yml', 'temp2': ENV_PATH + 'mcc_temp2.yml',
    'relocate': ENV_PATH + 'mcc_relocate.yml', 'ngs_te_mapper': ENV_PATH +
    'mcc_ngs_te_mapper.yml', 'ngs_te_mapper2': ENV_PATH +
    'mcc_ngs_te_mapper2.yml', 'popoolationte': ENV_PATH +
    'mcc_popoolationte.yml', 'popoolationte2': ENV_PATH +
    'mcc_popoolationte2.yml', 'relocate2': ENV_PATH + 'mcc_relocate2.yml',
    'tepid': ENV_PATH + 'mcc_tepid.yml', 'teflon': ENV_PATH +
    'mcc_teflon.yml', 'jitterbug': ENV_PATH + 'mcc_jitterbug.yml',
    'setup_reads': ENV_PATH + 'mcc_trimgalore.yml', 'processing': ENV_PATH +
    'mcc_map_reads.yml', 'map_reads': ENV_PATH + 'mcc_map_reads.yml',
    'trimgalore': ENV_PATH + 'mcc_trimgalore.yml', 'tebreak': ENV_PATH +
    'mcc_tebreak.yml'}
INSTALL_PATH = '{{inspath}}'
OUTPUT = {'coverage': INSTALL_PATH + 'tools/coverage/coverage.log',
    'te-locate': INSTALL_PATH + 'tools/te-locate/TE_locate.pl', 'retroseq':
    INSTALL_PATH + 'tools/retroseq/bin/retroseq.pl', 'temp': INSTALL_PATH +
    'tools/temp/scripts/TEMP_Insertion.sh', 'temp2': INSTALL_PATH +
    'tools/temp2/TEMP2', 'relocate': INSTALL_PATH +
    'tools/relocate/scripts/relocaTE_insertionFinder.pl', 'ngs_te_mapper': 
    INSTALL_PATH + 'tools/ngs_te_mapper/sourceCode/run_ngs_te_mapper.sh',
    'ngs_te_mapper2': INSTALL_PATH +
    'tools/ngs_te_mapper2/sourceCode/ngs_te_mapper2.py', 'popoolationte': 
    INSTALL_PATH + 'tools/popoolationte/identify-te-insertsites.pl',
    'popoolationte2': INSTALL_PATH +
    'tools/popoolationte2/popte2-v1.10.03.jar', 'relocate2': INSTALL_PATH +
    'tools/relocate2/scripts/relocaTE2.py', 'tepid': INSTALL_PATH +
    'tools/tepid/tepid-map', 'teflon': INSTALL_PATH +
    'tools/teflon/teflon.v0.4.py', 'jitterbug': INSTALL_PATH +
    'tools/jitterbug/jitterbug.py', 'map_reads': INSTALL_PATH +
    'tools/map_reads/map_reads.log', 'trimgalore': INSTALL_PATH +
    'tools/trimgalore/trimgalore.log', 'tebreak': INSTALL_PATH +
    'tools/tebreak/tebreak/tebreak'}

URL = {
    "te-locate" : "https://downloads.sourceforge.net/project/te-locate/TE-locate.tar",
    "retroseq" : "https://github.com/tk2/RetroSeq/archive/9d4f3b5270af2383f40e6e7ea1204ea718365db2.zip",
    "temp" : "https://github.com/JialiUMassWengLab/TEMP/archive/4f67e1da836721a9f0999efa52e1e648fedb75fc.zip",
    "temp2": "https://github.com/weng-lab/TEMP2/archive/4d25d050dc7832b82374502573e882a242457a0c.zip",
    "relocate" : "https://github.com/srobb1/RelocaTE/archive/ce3a2066e15f5c14e2887fdf8dce0485e1750e5b.zip",
    "ngs_te_mapper" : "https://github.com/bergmanlab/ngs_te_mapper/archive/f9f48996ac346ac86d57edbd00534aa1227b753e.zip",
    "ngs_te_mapper2": "https://github.com/bergmanlab/ngs_te_mapper2/archive/220619a3dd00b8c05c3b96328eb2424c6aad623e.zip",
    "popoolationte" : "http://downloads.sourceforge.net/project/popoolationte/popoolationte_1.02.zip",
    "popoolationte2": "http://downloads.sourceforge.net/project/popoolation-te2/popte2-v1.10.03.jar",
    "relocate2" : "https://github.com/stajichlab/RelocaTE2/archive/v2.0.1.zip",
    "tepid" : "https://github.com/ListerLab/TEPID/archive/ad46d65b5c41bf8a9171215d49b3ffaecdceaab0.zip",
    "teflon": "https://github.com/jradrion/TEFLoN/archive/3e2d67886b70644fd1f7d79263b3c8dbed639e46.zip",
    "jitterbug": "https://github.com/elzbth/jitterbug/archive/b6b3f9c7ee4af042d4410137269f174a1399b752.zip",
    "tebreak": "https://github.com/adamewing/tebreak/archive/3f00badda822dcb6390bbea5a6a1e233cff3e99c.zip"
}

MD5 = {
    "te-locate" : "c28e3dd7be89a8efcfbca8939923787c",
    "retroseq" : "54030657dd8476f1a65f5f71e809b4c3",
    "temp" : "f06e25244e9979510a9743bcd9c841a5",
    "temp2" : "55b6449113e85540f8a39bb02cfec9b0",
    "relocate" : "64cc60f65154368518529fb57becc3d6",
    "ngs_te_mapper" : "a00e9962ee3daca9fac915c23c6af203",
    "ngs_te_mapper2": "95198ab68fcb4f9dc267460a7f906fae",
    "popoolationte" : "315d266bd6da7487c919576dc46b92b4",
    "popoolationte2": "0c06186f0b1df215949f57a5cbb2d039",
    "relocate2" : "63eb7dbc09ffeb4063aef4857d198b06",
    "tepid" : "51f61acf138b07842074f054aba780d5",
    "teflon" : "a29d2e7411fd06778186ba322f51fdc9",
    "jitterbug": "05f165fb6a79a7a611d09981a355d27e",
    "tebreak": "ac475d3cc4b0435f0a333c8d86f57d3f"
}

ENV_PATH = "{{envpath}}"
ENV = {
    "coverage" : ENV_PATH+"mcc_coverage.yml",
    "te-locate" : ENV_PATH+"mcc_telocate.yml",
    "retroseq" : ENV_PATH+"mcc_retroseq.yml",
    "temp" : ENV_PATH+"mcc_temp.yml",
    "temp2" : ENV_PATH+"mcc_temp2.yml",
    "relocate" : ENV_PATH+"mcc_relocate.yml",
    "ngs_te_mapper" : ENV_PATH+"mcc_ngs_te_mapper.yml",
    "ngs_te_mapper2": ENV_PATH+"mcc_ngs_te_mapper2.yml",
    "popoolationte" : ENV_PATH+"mcc_popoolationte.yml",
    "popoolationte2" : ENV_PATH+"mcc_popoolationte2.yml",
    "relocate2" : ENV_PATH+"mcc_relocate2.yml",
    "tepid" : ENV_PATH+"mcc_tepid.yml",
    "teflon" : ENV_PATH+"mcc_teflon.yml",
    "jitterbug": ENV_PATH+"mcc_jitterbug.yml",
    "setup_reads": ENV_PATH+"mcc_trimgalore.yml",
    "processing":  ENV_PATH+"mcc_map_reads.yml",
    "map_reads": ENV_PATH+"mcc_map_reads.yml",
    "trimgalore": ENV_PATH+"mcc_trimgalore.yml",
    "tebreak": ENV_PATH+"mcc_tebreak.yml"
}

INSTALL_PATH = "{{inspath}}"
OUTPUT = {
    "coverage" : INSTALL_PATH+"tools/coverage/coverage.log",
    "te-locate" : INSTALL_PATH+"tools/te-locate/TE_locate.pl",
    "retroseq" : INSTALL_PATH+"tools/retroseq/bin/retroseq.pl",
    "temp" : INSTALL_PATH+"tools/temp/scripts/TEMP_Insertion.sh",
    "temp2" : INSTALL_PATH+"tools/temp2/TEMP2",
    "relocate" : INSTALL_PATH+"tools/relocate/scripts/relocaTE_insertionFinder.pl",
    "ngs_te_mapper" : INSTALL_PATH+"tools/ngs_te_mapper/sourceCode/run_ngs_te_mapper.sh",
    "ngs_te_mapper2": INSTALL_PATH+"tools/ngs_te_mapper2/sourceCode/ngs_te_mapper2.py",
    "popoolationte" : INSTALL_PATH+"tools/popoolationte/identify-te-insertsites.pl",
    "popoolationte2" : INSTALL_PATH+"tools/popoolationte2/popte2-v1.10.03.jar",
    "relocate2" : INSTALL_PATH+"tools/relocate2/scripts/relocaTE2.py",
    "tepid" : INSTALL_PATH+"tools/tepid/tepid-map",
    "teflon" : INSTALL_PATH+"tools/teflon/teflon.v0.4.py",
    "jitterbug": INSTALL_PATH+"tools/jitterbug/jitterbug.py",
    "map_reads" : INSTALL_PATH+"tools/map_reads/map_reads.log",
    "trimgalore" : INSTALL_PATH+"tools/trimgalore/trimgalore.log",
    "tebreak" : INSTALL_PATH+"tools/tebreak/tebreak/tebreak"
}
