Commit 1a3b4791 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 4.3a+dfsg

parent 01c82876

README_release.txt

+18 −63
Original line number Diff line number Diff line
@@ -6,79 +6,34 @@ 
0) Install required libraries



	# ANTRL

	curl -O http://www.antlr.org/download/antlr-4.5.1-complete.jar

	wget http://www.antlr.org/download/antlr-4.5.1-complete.jar

	mvn install:install-file -Dfile=antlr-4.5.1-complete.jar -DgroupId=org.antlr -DartifactId=antlr -Dversion=4.5.1 -Dpackaging=jar



	# BioJava

	wget http://biojava.org/download/maven/org/biojava/biojava3-core/3.0.7/biojava3-core-3.0.7.jar

	mvn install:install-file -Dfile=biojava3-core-3.0.7.jar      -DgroupId=org.biojava -DartifactId=biojava3-core      -Dversion=3.0.7 -Dpackaging=jar

	mvn install:install-file -Dfile=biojava3-structure-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-structure -Dversion=3.0.7 -Dpackaging=jar



1) Run JUnit tests (TestSuiteUnity) and make sure all of them pass



2) Run integration tests (TestSuiteIntegration)

	

3) Change version numbers:

	wget http://biojava.org/download/maven/org/biojava/biojava3-structure/3.0.7/biojava3-structure-3.0.7.jar

	mvn install:install-file -Dfile=biojava3-structure-3.0.7.jar -DgroupId=org.biojava -DartifactId=biojava3-structure -Dversion=3.0.7 -Dpackaging=jar



1) Change version numbers:

	- Update SnpEff pom.xml 

	- Update SnpSift pom.xml

	- Update scripts_build/config.sh 

	- Update scripts_build/make.bds



4) Build JAR files, download databases, build databases, etc.

	

	a) Build JAR files

		./scripts_build/make.sh 

	

	b) Nextprot:

	

		 - Check nextProt database: Any new release? 

				ftp://ftp.nextprot.org/pub/current_release/xml/

				

		 - Build nextProt database (WARNING: It takes a lot of memory!): 

		 

		 	java -Xmx50G -jar snpEff.jar buildNextProt -v GRCh37.71 db/nextProt 2>&1 | tee buildNextProt.out

		 	

	c) Motif (Jasper)

	

		- Download latest Jaspar database

		

			./scripts_build/download_Pwms_Jaspar.sh

				

		- Copy to latest GRCh and GRCm (or any that has a mofit file "ls data/*/motif*)

		

			cp db/jaspar/pwms.bin data/GRCh37.75/

			cp db/jaspar/pwms.bin data/GRCm38.78/

		

	d) Check if there is a newer dbNSFP

	

		https://sites.google.com/site/jpopgen/dbNSFP



	e) Download ENSEMBL genomes



		./scripts_build/download_ensembl.sh

		./scripts_build/download_ensembl_bfmpp.sh



	f) Download NCBI genomes



		./scripts_build/download_ncbi.sh

		

	g) Download NCBI Human genomes



		./scripts_build/download_hg19.sh

		./scripts_build/download_hg19kg.sh



		./scripts_build/download_hg38.sh

		./scripts_build/download_hg38kg.sh



2) Build JAR files, download databases, build databases, etc.

		./make.bds 



5) Upload files to sourceForge

3) Run JUnit tests and integration tests

	./make.bds -test



	./scripts_build/uploadSourceForge.sh

4) Download databases: ENSEMBL, NCBI, dbSnp, ClinVar, dbNSFP, PDB, Jaspar, etc.

		./make.bds -download

		 		

6) Update Galaxy's snpEff.xml

		# Create galaxy genomes list 

		scripts_build/galaxy.sh		 

5) Build databases

		./make.bds -db

			

7) Upload to Galaxy ToolShed: http://toolshed.g2.bx.psu.edu/

		Reference: http://wiki.g2.bx.psu.edu/Tool%20Shed

6) Upload files to sourceForge



	./make.bds -uploadCore		# Upload core files

	./make.bds -uploadDbs		# Upload databases files

	./make.bds -uploadHtml		# Upload web pages and manual

config/snpEff.ENSEMBL_75.config

+1 −71
Original line number Diff line number Diff line 
#---

# Ensembl 75 versions 

#---



ailMel1.75.genome : Ailuropoda_melanoleuca

ailMel1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



BGI_duck_1.0.75.genome : Anas_platyrhynchos

BGI_duck_1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



AnoCar2.0.75.genome : Anolis_carolinensis

AnoCar2.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



AstMex102.75.genome : Astyanax_mexicanus

AstMex102.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



UMD3.1.75.genome : Bos_taurus

UMD3.1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



WBcel235.75.genome : Caenorhabditis_elegans

WBcel235.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



C_jacchus3.2.1.75.genome : Callithrix_jacchus

C_jacchus3.2.1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



CanFam3.1.75.genome : Canis_familiaris

CanFam3.1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



cavPor3.75.genome : Cavia_porcellus

cavPor3.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



choHof1.75.genome : Choloepus_hoffmanni

choHof1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



KH.75.genome : Ciona_intestinalis

KH.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



CSAV2.0.75.genome : Ciona_savignyi

CSAV2.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Zv9.75.genome : Danio_rerio

Zv9.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Dasnov3.0.75.genome : Dasypus_novemcinctus

Dasnov3.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



dipOrd1.75.genome : Dipodomys_ordii

dipOrd1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



BDGP5.75.genome : Drosophila_melanogaster

BDGP5.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



TENREC.75.genome : Echinops_telfairi

TENREC.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



EquCab2.75.genome : Equus_caballus

EquCab2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



HEDGEHOG.75.genome : Erinaceus_europaeus

HEDGEHOG.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Felis_catus_6.2.75.genome : Felis_catus

Felis_catus_6.2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



FicAlb_1.4.75.genome : Ficedula_albicollis

FicAlb_1.4.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



gadMor1.75.genome : Gadus_morhua

gadMor1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Galgal4.75.genome : Gallus_gallus

Galgal4.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



BROADS1.75.genome : Gasterosteus_aculeatus

BROADS1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



gorGor3.1.75.genome : Gorilla_gorilla

gorGor3.1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



GRCh37.75.genome : Homo_sapiens

GRCh37.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



spetri2.75.genome : Ictidomys_tridecemlineatus

spetri2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



LatCha1.75.genome : Latimeria_chalumnae

LatCha1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



LepOcu1.75.genome : Lepisosteus_oculatus

LepOcu1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



loxAfr3.75.genome : Loxodonta_africana

loxAfr3.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



MMUL_1.75.genome : Macaca_mulatta

MMUL_1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Meug_1.0.75.genome : Macropus_eugenii

Meug_1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



UMD2.75.genome : Meleagris_gallopavo

UMD2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



micMur1.75.genome : Microcebus_murinus

micMur1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



BROADO5.75.genome : Monodelphis_domestica

BROADO5.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



GRCm38.75.genome : Mus_musculus

GRCm38.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



MusPutFur1.0.75.genome : Mustela_putorius_furo

MusPutFur1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Myoluc2.0.75.genome : Myotis_lucifugus

Myoluc2.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Nleu1.0.75.genome : Nomascus_leucogenys

Nleu1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



pika.75.genome : Ochotona_princeps

pika.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Orenil1.0.75.genome : Oreochromis_niloticus

Orenil1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



OANA5.75.genome : Ornithorhynchus_anatinus

OANA5.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



OryCun2.0.75.genome : Oryctolagus_cuniculus

OryCun2.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



MEDAKA1.75.genome : Oryzias_latipes

MEDAKA1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



OtoGar3.75.genome : Otolemur_garnettii

OtoGar3.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Oar_v3.1.75.genome : Ovis_aries

Oar_v3.1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



CHIMP2.1.4.75.genome : Pan_troglodytes

CHIMP2.1.4.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



PelSin_1.0.75.genome : Pelodiscus_sinensis

PelSin_1.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Pmarinus_7.0.75.genome : Petromyzon_marinus

Pmarinus_7.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



PPYG2.75.genome : Pongo_abelii

PPYG2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



proCap1.75.genome : Procavia_capensis

proCap1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



pteVam1.75.genome : Pteropus_vampyrus

pteVam1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Rnor_5.0.75.genome : Rattus_norvegicus

Rnor_5.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



R64-1-1.75.genome : Saccharomyces_cerevisiae

R64-1-1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



DEVIL7.0.75.genome : Sarcophilus_harrisii

DEVIL7.0.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



COMMON_SHREW1.75.genome : Sorex_araneus

COMMON_SHREW1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Sscrofa10.2.75.genome : Sus_scrofa

Sscrofa10.2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



taeGut3.2.4.75.genome : Taeniopygia_guttata

taeGut3.2.4.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



FUGU4.75.genome : Takifugu_rubripes

FUGU4.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



tarSyr1.75.genome : Tarsius_syrichta

tarSyr1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



TETRAODON8.75.genome : Tetraodon_nigroviridis

TETRAODON8.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



TREESHREW.75.genome : Tupaia_belangeri

TREESHREW.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



turTru1.75.genome : Tursiops_truncatus

turTru1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



vicPac1.75.genome : Vicugna_pacos

vicPac1.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



JGI_4.2.75.genome : Xenopus_tropicalis

JGI_4.2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/



Xipmac4.4.2.75.genome : Xiphophorus_maculatus

Xipmac4.4.2.75.reference : ftp://ftp.ensembl.org/pub/release-75/gtf/
 
 No newline at end of file

config/snpEff.ENSEMBL_78.config

deleted100644 → 0
+0 −207
Original line number Diff line number Diff line 
ailMel1.78.genome : Ailuropoda_melanoleuca

ailMel1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



BGI_duck_1.0.78.genome : Anas_platyrhynchos

BGI_duck_1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



AnoCar2.0.78.genome : Anolis_carolinensis

AnoCar2.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



AstMex102.78.genome : Astyanax_mexicanus

AstMex102.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



UMD3.1.78.genome : Bos_taurus

UMD3.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



WBcel235.78.genome : Caenorhabditis_elegans

WBcel235.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



C_jacchus3.2.1.78.genome : Callithrix_jacchus

C_jacchus3.2.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



CanFam3.1.78.genome : Canis_familiaris

CanFam3.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



cavPor3.78.genome : Cavia_porcellus

cavPor3.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



ChlSab1.1.78.genome : Chlorocebus_sabaeus

ChlSab1.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



choHof1.78.genome : Choloepus_hoffmanni

choHof1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



KH.78.genome : Ciona_intestinalis

KH.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



CSAV2.0.78.genome : Ciona_savignyi

CSAV2.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Zv9.78.genome : Danio_rerio

Zv9.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Dasnov3.0.78.genome : Dasypus_novemcinctus

Dasnov3.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



dipOrd1.78.genome : Dipodomys_ordii

dipOrd1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



BDGP5.78.genome : Drosophila_melanogaster

BDGP5.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



TENREC.78.genome : Echinops_telfairi

TENREC.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



EquCab2.78.genome : Equus_caballus

EquCab2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



HEDGEHOG.78.genome : Erinaceus_europaeus

HEDGEHOG.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Felis_catus_6.2.78.genome : Felis_catus

Felis_catus_6.2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



FicAlb_1.4.78.genome : Ficedula_albicollis

FicAlb_1.4.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



gadMor1.78.genome : Gadus_morhua

gadMor1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Galgal4.78.genome : Gallus_gallus

Galgal4.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



BROADS1.78.genome : Gasterosteus_aculeatus

BROADS1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



gorGor3.1.78.genome : Gorilla_gorilla

gorGor3.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



GRCh38.78.genome : Homo_sapiens

GRCh38.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



spetri2.78.genome : Ictidomys_tridecemlineatus

spetri2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



LatCha1.78.genome : Latimeria_chalumnae

LatCha1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



LepOcu1.78.genome : Lepisosteus_oculatus

LepOcu1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



loxAfr3.78.genome : Loxodonta_africana

loxAfr3.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



MMUL_1.78.genome : Macaca_mulatta

MMUL_1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Meug_1.0.78.genome : Macropus_eugenii

Meug_1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



UMD2.78.genome : Meleagris_gallopavo

UMD2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



micMur1.78.genome : Microcebus_murinus

micMur1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



BROADO5.78.genome : Monodelphis_domestica

BROADO5.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



GRCm38.78.genome : Mus_musculus

GRCm38.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



MusPutFur1.0.78.genome : Mustela_putorius_furo

MusPutFur1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Myoluc2.0.78.genome : Myotis_lucifugus

Myoluc2.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Nleu1.0.78.genome : Nomascus_leucogenys

Nleu1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



pika.78.genome : Ochotona_princeps

pika.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Orenil1.0.78.genome : Oreochromis_niloticus

Orenil1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



OANA5.78.genome : Ornithorhynchus_anatinus

OANA5.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



OryCun2.0.78.genome : Oryctolagus_cuniculus

OryCun2.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



MEDAKA1.78.genome : Oryzias_latipes

MEDAKA1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



OtoGar3.78.genome : Otolemur_garnettii

OtoGar3.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Oar_v3.1.78.genome : Ovis_aries

Oar_v3.1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



CHIMP2.1.4.78.genome : Pan_troglodytes

CHIMP2.1.4.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



PapAnu2.0.78.genome : Papio_anubis

PapAnu2.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



PelSin_1.0.78.genome : Pelodiscus_sinensis

PelSin_1.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Pmarinus_7.0.78.genome : Petromyzon_marinus

Pmarinus_7.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



PoeFor_5.1.2.78.genome : Poecilia_formosa

PoeFor_5.1.2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



PPYG2.78.genome : Pongo_abelii

PPYG2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



proCap1.78.genome : Procavia_capensis

proCap1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



pteVam1.78.genome : Pteropus_vampyrus

pteVam1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Rnor_5.0.78.genome : Rattus_norvegicus

Rnor_5.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



R64-1-1.78.genome : Saccharomyces_cerevisiae

R64-1-1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



DEVIL7.0.78.genome : Sarcophilus_harrisii

DEVIL7.0.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



COMMON_SHREW1.78.genome : Sorex_araneus

COMMON_SHREW1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Sscrofa10.2.78.genome : Sus_scrofa

Sscrofa10.2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



taeGut3.2.4.78.genome : Taeniopygia_guttata

taeGut3.2.4.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



FUGU4.78.genome : Takifugu_rubripes

FUGU4.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



tarSyr1.78.genome : Tarsius_syrichta

tarSyr1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



TETRAODON8.78.genome : Tetraodon_nigroviridis

TETRAODON8.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



TREESHREW.78.genome : Tupaia_belangeri

TREESHREW.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



turTru1.78.genome : Tursiops_truncatus

turTru1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



vicPac1.78.genome : Vicugna_pacos

vicPac1.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



JGI_4.2.78.genome : Xenopus_tropicalis

JGI_4.2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/



Xipmac4.4.2.78.genome : Xiphophorus_maculatus

Xipmac4.4.2.78.reference : ftp://ftp.ensembl.org/pub/release-78/gtf/

config/snpEff.ENSEMBL_79.config

deleted100644 → 0
+0 −207
Original line number Diff line number Diff line 
ailMel1.79.genome : Ailuropoda_melanoleuca

ailMel1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



BGI_duck_1.0.79.genome : Anas_platyrhynchos

BGI_duck_1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



AnoCar2.0.79.genome : Anolis_carolinensis

AnoCar2.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



AstMex102.79.genome : Astyanax_mexicanus

AstMex102.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



UMD3.1.79.genome : Bos_taurus

UMD3.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



WBcel235.79.genome : Caenorhabditis_elegans

WBcel235.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



C_jacchus3.2.1.79.genome : Callithrix_jacchus

C_jacchus3.2.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



CanFam3.1.79.genome : Canis_familiaris

CanFam3.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



cavPor3.79.genome : Cavia_porcellus

cavPor3.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



ChlSab1.1.79.genome : Chlorocebus_sabaeus

ChlSab1.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



choHof1.79.genome : Choloepus_hoffmanni

choHof1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



KH.79.genome : Ciona_intestinalis

KH.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



CSAV2.0.79.genome : Ciona_savignyi

CSAV2.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Zv9.79.genome : Danio_rerio

Zv9.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Dasnov3.0.79.genome : Dasypus_novemcinctus

Dasnov3.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



dipOrd1.79.genome : Dipodomys_ordii

dipOrd1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



BDGP6.79.genome : Drosophila_melanogaster

BDGP6.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



TENREC.79.genome : Echinops_telfairi

TENREC.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



EquCab2.79.genome : Equus_caballus

EquCab2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



HEDGEHOG.79.genome : Erinaceus_europaeus

HEDGEHOG.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Felis_catus_6.2.79.genome : Felis_catus

Felis_catus_6.2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



FicAlb_1.4.79.genome : Ficedula_albicollis

FicAlb_1.4.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



gadMor1.79.genome : Gadus_morhua

gadMor1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Galgal4.79.genome : Gallus_gallus

Galgal4.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



BROADS1.79.genome : Gasterosteus_aculeatus

BROADS1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



gorGor3.1.79.genome : Gorilla_gorilla

gorGor3.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



GRCh38.79.genome : Homo_sapiens

GRCh38.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



spetri2.79.genome : Ictidomys_tridecemlineatus

spetri2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



LatCha1.79.genome : Latimeria_chalumnae

LatCha1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



LepOcu1.79.genome : Lepisosteus_oculatus

LepOcu1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



loxAfr3.79.genome : Loxodonta_africana

loxAfr3.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



MMUL_1.79.genome : Macaca_mulatta

MMUL_1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Meug_1.0.79.genome : Macropus_eugenii

Meug_1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



UMD2.79.genome : Meleagris_gallopavo

UMD2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



micMur1.79.genome : Microcebus_murinus

micMur1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



BROADO5.79.genome : Monodelphis_domestica

BROADO5.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



GRCm38.79.genome : Mus_musculus

GRCm38.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



MusPutFur1.0.79.genome : Mustela_putorius_furo

MusPutFur1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Myoluc2.0.79.genome : Myotis_lucifugus

Myoluc2.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Nleu1.0.79.genome : Nomascus_leucogenys

Nleu1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



pika.79.genome : Ochotona_princeps

pika.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Orenil1.0.79.genome : Oreochromis_niloticus

Orenil1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



OANA5.79.genome : Ornithorhynchus_anatinus

OANA5.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



OryCun2.0.79.genome : Oryctolagus_cuniculus

OryCun2.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



MEDAKA1.79.genome : Oryzias_latipes

MEDAKA1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



OtoGar3.79.genome : Otolemur_garnettii

OtoGar3.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Oar_v3.1.79.genome : Ovis_aries

Oar_v3.1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



CHIMP2.1.4.79.genome : Pan_troglodytes

CHIMP2.1.4.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



PapAnu2.0.79.genome : Papio_anubis

PapAnu2.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



PelSin_1.0.79.genome : Pelodiscus_sinensis

PelSin_1.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Pmarinus_7.0.79.genome : Petromyzon_marinus

Pmarinus_7.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



PoeFor_5.1.2.79.genome : Poecilia_formosa

PoeFor_5.1.2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



PPYG2.79.genome : Pongo_abelii

PPYG2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



proCap1.79.genome : Procavia_capensis

proCap1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



pteVam1.79.genome : Pteropus_vampyrus

pteVam1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Rnor_5.0.79.genome : Rattus_norvegicus

Rnor_5.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



R64-1-1.79.genome : Saccharomyces_cerevisiae

R64-1-1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



DEVIL7.0.79.genome : Sarcophilus_harrisii

DEVIL7.0.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



COMMON_SHREW1.79.genome : Sorex_araneus

COMMON_SHREW1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Sscrofa10.2.79.genome : Sus_scrofa

Sscrofa10.2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



taeGut3.2.4.79.genome : Taeniopygia_guttata

taeGut3.2.4.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



FUGU4.79.genome : Takifugu_rubripes

FUGU4.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



tarSyr1.79.genome : Tarsius_syrichta

tarSyr1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



TETRAODON8.79.genome : Tetraodon_nigroviridis

TETRAODON8.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



TREESHREW.79.genome : Tupaia_belangeri

TREESHREW.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



turTru1.79.genome : Tursiops_truncatus

turTru1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



vicPac1.79.genome : Vicugna_pacos

vicPac1.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



JGI_4.2.79.genome : Xenopus_tropicalis

JGI_4.2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/



Xipmac4.4.2.79.genome : Xiphophorus_maculatus

Xipmac4.4.2.79.reference : ftp://ftp.ensembl.org/pub/release-79/gtf/

config/snpEff.ENSEMBL_81.config

deleted100644 → 0
+0 −138

File deleted.

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