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Merge pull request #109 from bluegenes/patch-1
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fix conda recipe and busco download issues
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@camillescott
camillescott authored Jun 18, 2018
2 parents 46de37a + a9b39eb commit 66a1b98
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88 changes: 44 additions & 44 deletions dammit/databases.json
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Original file line number Diff line number Diff line change
Expand Up @@ -51,308 +51,308 @@

"BUSCO": {
"deltaepsilonsub": {
"url": "http://busco.ezlab.org/v2/datasets/deltaepsilonsub_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/deltaepsilonsub_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "deltaepsilonsub_odb9",
"db_type": "BUSCO"
},
"basidiomycota": {
"url": "http://busco.ezlab.org/v2/datasets/basidiomycota_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/basidiomycota_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "basidiomycota_odb9",
"db_type": "BUSCO"
},
"bacteria": {
"url": "http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "bacteria_odb9",
"db_type": "BUSCO"
},
"dikarya": {
"url": "http://busco.ezlab.org/v2/datasets/dikarya_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/dikarya_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "dikarya_odb9",
"db_type": "BUSCO"
},
"fungi": {
"url": "http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "fungi_odb9",
"db_type": "BUSCO"
},
"eurotiomycetes": {
"url": "http://busco.ezlab.org/v2/datasets/eurotiomycetes_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/eurotiomycetes_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "eurotiomycetes_odb9",
"db_type": "BUSCO"
},
"alveolata_stramenophiles": {
"url": "http://busco.ezlab.org/v2/datasets/alveolata_stramenophiles_ensembl.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/alveolata_stramenophiles_ensembl.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "alveolata_stramenophiles_ensembl",
"db_type": "BUSCO"
},
"pezizomycotina": {
"url": "http://busco.ezlab.org/v2/datasets/pezizomycotina_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/pezizomycotina_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "pezizomycotina_odb9",
"db_type": "BUSCO"
},
"proteobacteria": {
"url": "http://busco.ezlab.org/v2/datasets/proteobacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/proteobacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "proteobacteria_odb9",
"db_type": "BUSCO"
},
"laurasiatheria": {
"url": "http://busco.ezlab.org/v2/datasets/laurasiatheria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/laurasiatheria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "laurasiatheria_odb9",
"db_type": "BUSCO"
},
"arthropoda": {
"url": "http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "arthropoda_odb9",
"db_type": "BUSCO"
},
"tetrapoda": {
"url": "http://busco.ezlab.org/v2/datasets/tetrapoda_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/tetrapoda_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "tetrapoda_odb9",
"db_type": "BUSCO"
},
"clostridia": {
"url": "http://busco.ezlab.org/v2/datasets/clostridia_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/clostridia_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "clostridia_odb9",
"db_type": "BUSCO"
},
"protists": {
"url": "http://busco.ezlab.org/v2/datasets/protists_ensembl.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/protists_ensembl.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "protists_ensembl",
"db_type": "BUSCO"
},
"enterobacteriales": {
"url": "http://busco.ezlab.org/v2/datasets/enterobacteriales_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/enterobacteriales_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "enterobacteriales_odb9",
"db_type": "BUSCO"
},
"gammaproteobacteria": {
"url": "http://busco.ezlab.org/v2/datasets/gammaproteobacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/gammaproteobacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "gammaproteobacteria_odb9",
"db_type": "BUSCO"
},
"mammalia": {
"url": "http://busco.ezlab.org/v2/datasets/mammalia_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/mammalia_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "mammalia_odb9",
"db_type": "BUSCO"
},
"rhizobiales": {
"url": "http://busco.ezlab.org/v2/datasets/rhizobiales_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/rhizobiales_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "rhizobiales_odb9",
"db_type": "BUSCO"
},
"nematoda": {
"url": "http://busco.ezlab.org/v2/datasets/nematoda_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/nematoda_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "nematoda_odb9",
"db_type": "BUSCO"
},
"tenericutes": {
"url": "http://busco.ezlab.org/v2/datasets/tenericutes_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/tenericutes_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "tenericutes_odb9",
"db_type": "BUSCO"
},
"saccharomyceta": {
"url": "http://busco.ezlab.org/v2/datasets/saccharomyceta_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/saccharomyceta_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "saccharomyceta_odb9",
"db_type": "BUSCO"
},
"saccharomycetales": {
"url": "http://busco.ezlab.org/v2/datasets/saccharomycetales_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/saccharomycetales_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "saccharomycetales_odb9",
"db_type": "BUSCO"
},
"firmicutes": {
"url": "http://busco.ezlab.org/v2/datasets/firmicutes_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/firmicutes_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "firmicutes_odb9",
"db_type": "BUSCO"
},
"bacteroidetes": {
"url": "http://busco.ezlab.org/v2/datasets/bacteroidetes_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/bacteroidetes_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "bacteroidetes_odb9",
"db_type": "BUSCO"
},
"sordariomyceta": {
"url": "http://busco.ezlab.org/v2/datasets/sordariomyceta_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/sordariomyceta_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "sordariomyceta_odb9",
"db_type": "BUSCO"
},
"ascomycota": {
"url": "http://busco.ezlab.org/v2/datasets/ascomycota_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/ascomycota_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "ascomycota_odb9",
"db_type": "BUSCO"
},
"bacillales": {
"url": "http://busco.ezlab.org/v2/datasets/bacillales_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/bacillales_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "bacillales_odb9",
"db_type": "BUSCO"
},
"insecta": {
"url": "http://busco.ezlab.org/v2/datasets/insecta_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/insecta_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "insecta_odb9",
"db_type": "BUSCO"
},
"diptera": {
"url": "http://busco.ezlab.org/v2/datasets/diptera_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/diptera_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "diptera_odb9",
"db_type": "BUSCO"
},
"actinopterygii": {
"url": "http://busco.ezlab.org/v2/datasets/actinopterygii_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/actinopterygii_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "actinopterygii_odb9",
"db_type": "BUSCO"
},
"hymenoptera": {
"url": "http://busco.ezlab.org/v2/datasets/hymenoptera_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/hymenoptera_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "hymenoptera_odb9",
"db_type": "BUSCO"
},
"euarchontoglires": {
"url": "http://busco.ezlab.org/v2/datasets/euarchontoglires_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/euarchontoglires_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "euarchontoglires_odb9",
"db_type": "BUSCO"
},
"aves": {
"url": "http://busco.ezlab.org/v2/datasets/aves_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/aves_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "aves_odb9",
"db_type": "BUSCO"
},
"betaproteobacteria": {
"url": "http://busco.ezlab.org/v2/datasets/betaproteobacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/betaproteobacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "betaproteobacteria_odb9",
"db_type": "BUSCO"
},
"cyanobacteria": {
"url": "http://busco.ezlab.org/v2/datasets/cyanobacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/cyanobacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "cyanobacteria_odb9",
"db_type": "BUSCO"
},
"endopterygota": {
"url": "http://busco.ezlab.org/v2/datasets/endopterygota_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/endopterygota_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "endopterygota_odb9",
"db_type": "BUSCO"
},
"embryophyta": {
"url": "http://busco.ezlab.org/v2/datasets/embryophyta_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/embryophyta_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "embryophyta_odb9",
"db_type": "BUSCO"
},
"microsporidia": {
"url": "http://busco.ezlab.org/v2/datasets/microsporidia_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/microsporidia_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "microsporidia_odb9",
"db_type": "BUSCO"
},
"lactobacillales": {
"url": "http://busco.ezlab.org/v2/datasets/lactobacillales_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/lactobacillales_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "lactobacillales_odb9",
"db_type": "BUSCO"
},
"eukaryota": {
"url": "http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "eukaryota_odb9",
"db_type": "BUSCO"
},
"metazoa": {
"url": "http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "metazoa_odb9",
"db_type": "BUSCO"
},
"actinobacteria": {
"url": "http://busco.ezlab.org/v2/datasets/actinobacteria_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/actinobacteria_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "actinobacteria_odb9",
"db_type": "BUSCO"
},
"spirochaetes": {
"url": "http://busco.ezlab.org/v2/datasets/spirochaetes_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/spirochaetes_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "spirochaetes_odb9",
"db_type": "BUSCO"
},
"vertebrata": {
"url": "http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz",
"url": "https://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz",
"access": "download",
"fileformat": "tar.gz",
"folder": "vertebrata_odb9",
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5 changes: 3 additions & 2 deletions recipe/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ requirements:
# Other
- infernal
- hmmer
- transdecoder
- transdecoder ==3.0.1
- last
- busco ==3.0.2

Expand All @@ -51,10 +51,11 @@ requirements:
# Other
- infernal
- hmmer
- transdecoder
- transdecoder ==3.0.1
- last
- busco ==3.0.2
- parallel
- bioconductor-seqlogo

test:
imports:
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