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.classpath
View file @ da15a77f
......@@ -22,10 +22,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
.gitignore
View file @ da15a77f
......@@ -3,3 +3,4 @@
/target
snpEff_genes.txt
snpEff_summary.html
**/*.swp
.settings/org.eclipse.jdt.core.prefs
View file @ da15a77f
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.7
org.eclipse.jdt.core.compiler.source=1.8
config/snpEff.ENSEMBL_86.config 0 → 100644
View file @ da15a77f
ailMel1.86.genome : Ailuropoda_melanoleuca
ailMel1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
BGI_duck_1.0.86.genome : Anas_platyrhynchos
BGI_duck_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
AnoCar2.0.86.genome : Anolis_carolinensis
AnoCar2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
AstMex102.86.genome : Astyanax_mexicanus
AstMex102.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
UMD3.1.86.genome : Bos_taurus
UMD3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
WBcel235.86.genome : Caenorhabditis_elegans
WBcel235.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
C_jacchus3.2.1.86.genome : Callithrix_jacchus
C_jacchus3.2.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
CanFam3.1.86.genome : Canis_familiaris
CanFam3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
cavPor3.86.genome : Cavia_porcellus
cavPor3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
ChlSab1.1.86.genome : Chlorocebus_sabaeus
ChlSab1.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
choHof1.86.genome : Choloepus_hoffmanni
choHof1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
KH.86.genome : Ciona_intestinalis
KH.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
CSAV2.0.86.genome : Ciona_savignyi
CSAV2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
GRCz10.86.genome : Danio_rerio
GRCz10.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Dasnov3.0.86.genome : Dasypus_novemcinctus
Dasnov3.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
dipOrd1.86.genome : Dipodomys_ordii
dipOrd1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
BDGP6.86.genome : Drosophila_melanogaster
BDGP6.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
TENREC.86.genome : Echinops_telfairi
TENREC.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
EquCab2.86.genome : Equus_caballus
EquCab2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
HEDGEHOG.86.genome : Erinaceus_europaeus
HEDGEHOG.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Felis_catus_6.2.86.genome : Felis_catus
Felis_catus_6.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
FicAlb_1.4.86.genome : Ficedula_albicollis
FicAlb_1.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
gadMor1.86.genome : Gadus_morhua
gadMor1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Gallus_gallus-5.0.86.genome : Gallus_gallus
Gallus_gallus-5.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
BROADS1.86.genome : Gasterosteus_aculeatus
BROADS1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
gorGor3.1.86.genome : Gorilla_gorilla
gorGor3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
GRCh38.86.genome : Homo_sapiens
GRCh38.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
spetri2.86.genome : Ictidomys_tridecemlineatus
spetri2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
LatCha1.86.genome : Latimeria_chalumnae
LatCha1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
LepOcu1.86.genome : Lepisosteus_oculatus
LepOcu1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
loxAfr3.86.genome : Loxodonta_africana
loxAfr3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Mmul_8.0.1.86.genome : Macaca_mulatta
Mmul_8.0.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Meug_1.0.86.genome : Macropus_eugenii
Meug_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
UMD2.86.genome : Meleagris_gallopavo
UMD2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Mmur_2.0.86.genome : Microcebus_murinus
Mmur_2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
BROADO5.86.genome : Monodelphis_domestica
BROADO5.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
GRCm38.86.genome : Mus_musculus
GRCm38.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
129S1_SvImJ_v1.86.genome : Mus_musculus_129s1svimj
129S1_SvImJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
A_J_v1.86.genome : Mus_musculus_aj
A_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
AKR_J_v1.86.genome : Mus_musculus_akrj
AKR_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
BALB_cJ_v1.86.genome : Mus_musculus_balbcj
BALB_cJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
C3H_HeJ_v1.86.genome : Mus_musculus_c3hhej
C3H_HeJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
C57BL_6NJ_v1.86.genome : Mus_musculus_c57bl6nj
C57BL_6NJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
CAST_EiJ_v1.86.genome : Mus_musculus_casteij
CAST_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
CBA_J_v1.86.genome : Mus_musculus_cbaj
CBA_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
DBA_2J_v1.86.genome : Mus_musculus_dba2j
DBA_2J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
FVB_NJ_v1.86.genome : Mus_musculus_fvbnj
FVB_NJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
LP_J_v1.86.genome : Mus_musculus_lpj
LP_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
NOD_ShiLtJ_v1.86.genome : Mus_musculus_nodshiltj
NOD_ShiLtJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
NZO_HlLtJ_v1.86.genome : Mus_musculus_nzohlltj
NZO_HlLtJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
PWK_PhJ_v1.86.genome : Mus_musculus_pwkphj
PWK_PhJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
WSB_EiJ_v1.86.genome : Mus_musculus_wsbeij
WSB_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
SPRET_EiJ_v1.86.genome : Mus_spretus_spreteij
SPRET_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
MusPutFur1.0.86.genome : Mustela_putorius_furo
MusPutFur1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Myoluc2.0.86.genome : Myotis_lucifugus
Myoluc2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Nleu1.0.86.genome : Nomascus_leucogenys
Nleu1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
pika.86.genome : Ochotona_princeps
pika.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Orenil1.0.86.genome : Oreochromis_niloticus
Orenil1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
OANA5.86.genome : Ornithorhynchus_anatinus
OANA5.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
OryCun2.0.86.genome : Oryctolagus_cuniculus
OryCun2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
MEDAKA1.86.genome : Oryzias_latipes
MEDAKA1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
OtoGar3.86.genome : Otolemur_garnettii
OtoGar3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Oar_v3.1.86.genome : Ovis_aries
Oar_v3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
CHIMP2.1.4.86.genome : Pan_troglodytes
CHIMP2.1.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
PapAnu2.0.86.genome : Papio_anubis
PapAnu2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
PelSin_1.0.86.genome : Pelodiscus_sinensis
PelSin_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Pmarinus_7.0.86.genome : Petromyzon_marinus
Pmarinus_7.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
PoeFor_5.1.2.86.genome : Poecilia_formosa
PoeFor_5.1.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
PPYG2.86.genome : Pongo_abelii
PPYG2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
proCap1.86.genome : Procavia_capensis
proCap1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
pteVam1.86.genome : Pteropus_vampyrus
pteVam1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Rnor_6.0.86.genome : Rattus_norvegicus
Rnor_6.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
R64-1-1.86.genome : Saccharomyces_cerevisiae
R64-1-1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
DEVIL7.0.86.genome : Sarcophilus_harrisii
DEVIL7.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
COMMON_SHREW1.86.genome : Sorex_araneus
COMMON_SHREW1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Sscrofa10.2.86.genome : Sus_scrofa
Sscrofa10.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
taeGut3.2.4.86.genome : Taeniopygia_guttata
taeGut3.2.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
FUGU4.86.genome : Takifugu_rubripes
FUGU4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
tarSyr1.86.genome : Tarsius_syrichta
tarSyr1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
TETRAODON8.86.genome : Tetraodon_nigroviridis
TETRAODON8.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
TREESHREW.86.genome : Tupaia_belangeri
TREESHREW.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
turTru1.86.genome : Tursiops_truncatus
turTru1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
vicPac1.86.genome : Vicugna_pacos
vicPac1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
JGI_4.2.86.genome : Xenopus_tropicalis
JGI_4.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
Xipmac4.4.2.86.genome : Xiphophorus_maculatus
Xipmac4.4.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
\ No newline at end of file
config/snpEff.NCBI.Felis_catus.config 0 → 100644
View file @ da15a77f
Felis_catus.genome : Felis_catus
Felis_catus.reference : ftp://ftp.ncbi.nih.gov/genomes/Felis_catus/
Felis_catus.retrieval_date : 2017-10-24
config/snpEff.NCBI.Takifugu_rubripes.config 0 → 100644
View file @ da15a77f
Takifugu_rubripes.genome : Takifugu_rubripes
Takifugu_rubripes.reference : ftp://ftp.ncbi.nih.gov/genomes/Takifugu_rubripes/
Takifugu_rubripes.retrieval_date : 2017-10-31
config/snpEff.core.config
View file @ da15a77f
......@@ -32,26 +32,25 @@ versions.url = http://snpeff.sourceforge.net/versions.txt
# Databases for human GRCh38 (hg38)
database.local.clinvar = ./db/GRCh38/clinvar/clinvar-latest.vcf.gz
database.clinvar.GRCh38 = ./db/GRCh38/clinvar/clinvar-latest.vcf.gz
database.repository.clinvar = ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar-latest.vcf.gz
database.local.dbsnp = ./db/GRCh38/dbSnp/dbSnp.vcf.gz
database.repository.dbsnp = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
database.dbsnp.GRCh38 = ./db/GRCh38/dbSnp/dbSnp.vcf.gz
database.repository.dbsnp.GRCH38 = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
database.local.dbnsfp = ./db/GRCh38/dbNSFP/dbNSFP.txt.gz
database.dbnsfp.GRCH38 = ./db/GRCh38/dbNSFP/dbNSFP.txt.gz
# # Databases for human GRCh37 (hg19)
# # Note: You must use this section if you are using old human genome
# database.local.clinvar = ./db/GRCh37/clinvar/clinvar-latest.vcf.gz
# database.repository.clinvar = ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar-latest.vcf.gz
#
# database.local.dbsnp = ./db/GRCh37/dbSnp/
# database.repository.dbsnp = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b141_GRCh37p13/VCF/
#
# database.local.gwascatalog = ./db/GRCh37/gwasCatalog/gwascatalog.txt
# database.repository.gwascatalog = http://www.genome.gov/admin/gwascatalog.txt
#
# database.local.dbnsfp = ./db/GRCh37/dbNSFP/dbNSFP.txt.gz
# Databases for human GRCh37 (hg19)
database.clinvar.GRCh37 = ./db/GRCh37/clinvar/clinvar-latest.vcf.gz
database.repository.clinvar.GRCh37 = ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar-latest.vcf.gz
database.dbsnp.GRCh37 = ./db/GRCh37/dbSnp/
database.repository.dbsnp.GRCh37 = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b141_GRCh37p13/VCF/
database.gwascatalog.GRCh37 = ./db/GRCh37/gwasCatalog/gwascatalog.txt
database.repository.gwascatalog.GRCh37 = http://www.genome.gov/admin/gwascatalog.txt
database.dbnsfp.GRCh37 = ./db/GRCh37/dbNSFP/dbNSFP.txt.gz
#-------------------------------------------------------------------------------
# Loss of function (LOF)
......
config/snpEff.dbs.config
View file @ da15a77f
This diff is collapsed.
config/snpEff.etc.config deleted 100644 → 0
View file @ 68f06f44
Source diff could not be displayed: it is too large. Options to address this: view the blob.
config/snpEff.test.config
View file @ da15a77f
......@@ -103,22 +103,26 @@ testNM_015296.genome : Test NM_015296.2
# HG38 using RefSeq: Problematic transcript in Chr6
test_hg38_NM_002117.genome : hg38 Chr6 NM_002117
#---
# Test cases: Non-human
#---
testMm37.61.genome : Mus_musculus
test_NC_031965.1.genome : Test from NC_031965.1
testAthalianaTair10.genome : Test using athaliana's genome ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release
testAP.genome : Test test_Adrian_Platts_vegi_genome
testChromoNamesDoNotMatch.genome: Test for genes not matching between GFF and FASTA
testEgrandis.genome : Test egrandis201 scaffold_5
testRice5.genome : Rice
testLukas.genome : Lukas_Schrader
testEmblPberghei.genome : Test_Embl_Pberghei
testAP.genome : Test test_Adrian_Platts_vegi_genome
testMaizeZmB73.genome : Test MaizeZmB73
testLukas.genome : Lukas_Schrader
testMacuminata.genome : Test macuminata_v2.180614
testChromoNamesDoNotMatch.genome: Test for genes not matching between GFF and FASTA
testMaizeZmB73.genome : Test MaizeZmB73
testMita.genome : Test Tetranychus urticae
testMm37.61.genome : Mus_musculus
testMycobacterium_tuberculosis_CCDC5079_uid203790.genome : Test for Mycobacterium_tuberculosis_CCDC5079_uid203790
testPaeru.PA14.genome : Test for Paeru PA14
testPpersica139.genome : Test for ppersica139
testRice5.genome : Rice
testVibrio.genome : Test case vibrio
#---
# Test for circular genomes
......@@ -140,4 +144,4 @@ test_too_many_chrs.genome : Genome having 10,000 chromosomes
#---
# Test cases: Quick tests and debugging
#---
test_zzz.genome: Test Zzz
config/ucsc.txt deleted 100644 → 0
View file @ 68f06f44
ailMel1
allMis1
anoCar2
anoGam1
apiMel2
apiMel3
aplCal1
aptMan1
balAcu1
bigZips
bosTau8
bosTauMd3
braFlo2
caeJap1
caePb2
caeRem3
calJac3
calMil1
canFam3
cavPor3
cb3
ce11
choHof1
chrPic1
ci2
criGri1
danRer10
dasNov3
dipOrd1
dm6
dp4
droAna3
droEre2
droGri2
droMoj3
droPer1
droSec1
droSim1
droVir3
droWil1
droYak2
eboVir3
echTel2
equCab2
eriEur2
felCat8
fr3
gadMor1
galGal5
galVar1
gasAcu1
geoFor1
gorGor4
hetGla2
hg19
hg38
latCha1
loxAfr3
macEug2
macFas5
melGal1
melUnd1
micMur2
mm10
mm9
monDom5
musFur1
myoLuc2
nomLeu3
ochPri3
oreNil2
ornAna2
oryCun2
oryLat2
otoGar1
otoGar3
oviAri3
panPan1
panTro4
papAnu2
papHam1
petMar1
petMar2
ponAbe2
priPac1
proCap1
pteVam1
rheMac8
rn6
sacCer3
saiBol1
sarHar1
sc1
sorAra2
speTri2
strPur2
susScr3
taeGut2
tarSyr2
tetNig2
triCas2
triMan1
tupBel1
turTru2
uniProt
venter1
vicPac2
visiGene
vsAilMel1
vsCanFam2
vsHg19
vsMm9
vsMonDom5
xenTro7
debian/changelog
View file @ da15a77f
snpeff (4.2+dfsg-1) UNRELEASED; urgency=low
snpeff (4.3t+dfsg-1) unstable; urgency=low
* Initial release (Closes: #<bug>)
-- Andreas Tille <tille@debian.org> Wed, 07 Nov 2012 17:01:35 +0100
-- Andreas Tille <tille@debian.org> Mon, 14 May 2018 22:07:57 +0200
debian/control
View file @ da15a77f
......@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
libtrove-java,
liblog4j2-java
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snpeff.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/snpeff.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/snpeff
Vcs-Git: https://salsa.debian.org/med-team/snpeff.git
Homepage: http://snpeff.sourceforge.net/
Package: snpeff
......
debian/copyright
View file @ da15a77f
......@@ -3,21 +3,19 @@ Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola@users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
Files-Excluded: */config/OLD
*/doc/*.pdf
*/doc/hgvs
*.jar
*/papers/*.pdf
*/scripts_build/OLD
Files: *
Copyright: © 2008-2016, Pablo Cingolani <pcingola@users.sourceforge.net>
License: LGPLv3
License: LGPL-3+
Files: debian/*
Copyright: © 2012 Andreas Tille <tille@debian.org>
License: LGPLv3
License: LGPL-3+
License: LGPLv3
License: LGPL-3+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
......
galaxy/tool-data/snpEff_genomes.loc
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git/update_force
View file @ da15a77f
#!/bin/sh -e
git fetch --all
git reset --hard origin/master
# Get current branch
branch=`git branch | grep '^*' | cut -f 2 -d ' '`
echo "Current branch is '$branch'"
# Reset to branch
git fetch --all
git reset --hard "origin/$branch"
git pull
hg38_refseq/test_hg38_NM_002117.build deleted 100644 → 0
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