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Removing ftp://gpftp.broadinstitute.org... and replacing with https:/…
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@liefeld
liefeld committed Feb 3, 2023
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66 changes: 66 additions & 0 deletions index_directory_htseq.json
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[
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Arabidopsis_thaliana_TAIR10_Ensembl.gtf", "label": "Arabidopsis_thaliana_TAIR10_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Arabidopsis_thaliana_TAIR10_NCBI.gtf", "label": "Arabidopsis_thaliana_TAIR10_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Arabidopsis_thaliana_TAIR9_Ensembl.gtf", "label": "Arabidopsis_thaliana_TAIR9_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Arabidopsis_thaliana_build9_1_NCBI.gtf", "label": "Arabidopsis_thaliana_build9_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bacillus_subtilis_168_EB2_Ensembl.gtf", "label": "Bacillus_subtilis_168_EB2_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_Btau_4_0_Ensembl.gtf", "label": "Bos_taurus_Btau_4_0_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_Btau_4_6_1_NCBI.gtf", "label": "Bos_taurus_Btau_4_6_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_UMD3_1_Ensembl.gtf", "label": "Bos_taurus_UMD3_1_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_UMD_3_1_NCBI.gtf", "label": "Bos_taurus_UMD_3_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_bosTau6_UCSC.gtf", "label": "Bos_taurus_bosTau6_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Bos_taurus_bosTau7_UCSC.gtf", "label": "Bos_taurus_bosTau7_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_WBcel215_Ensembl.gtf", "label": "Caenorhabditis_elegans_WBcel215_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_WS190_NCBI.gtf", "label": "Caenorhabditis_elegans_WS190_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_WS195_NCBI.gtf", "label": "Caenorhabditis_elegans_WS195_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_WS210_Ensembl.gtf", "label": "Caenorhabditis_elegans_WS210_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_WS220_Ensembl.gtf", "label": "Caenorhabditis_elegans_WS220_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_ce10_UCSC.gtf", "label": "Caenorhabditis_elegans_ce10_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Caenorhabditis_elegans_ce6_UCSC.gtf", "label": "Caenorhabditis_elegans_ce6_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_BROADD2_Ensembl.gtf", "label": "Canis_familiaris_BROADD2_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_CanFam3_1_Ensembl.gtf", "label": "Canis_familiaris_CanFam3_1_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_build2_1_NCBI.gtf", "label": "Canis_familiaris_build2_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_build3_1_NCBI.gtf", "label": "Canis_familiaris_build3_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_canFam2_UCSC.gtf", "label": "Canis_familiaris_canFam2_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Canis_familiaris_canFam3_UCSC.gtf", "label": "Canis_familiaris_canFam3_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Danio_rerio_Zv9_Ensembl.gtf", "label": "Danio_rerio_Zv9_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Danio_rerio_Zv9_NCBI.gtf", "label": "Danio_rerio_Zv9_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Danio_rerio_danRer7_UCSC.gtf", "label": "Danio_rerio_danRer7_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_BDGP5_25_Ensembl.gtf", "label": "Drosophila_melanogaster_BDGP5_25_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_BDGP5_Ensembl.gtf", "label": "Drosophila_melanogaster_BDGP5_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_build5_3_NCBI.gtf", "label": "Drosophila_melanogaster_build5_3_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_build5_41_NCBI.gtf", "label": "Drosophila_melanogaster_build5_41_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_build5_NCBI.gtf", "label": "Drosophila_melanogaster_build5_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Drosophila_melanogaster_dm3_UCSC.gtf", "label": "Drosophila_melanogaster_dm3_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Equus_caballus_EquCab2_0_NCBI.gtf", "label": "Equus_caballus_EquCab2_0_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Equus_caballus_EquCab2_Ensembl.gtf", "label": "Equus_caballus_EquCab2_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Equus_caballus_equCab2_UCSC.gtf", "label": "Equus_caballus_equCab2_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Escherichia_coli_K_12_DH10B_EB1_Ensembl.gtf", "label": "Escherichia_coli_K_12_DH10B_EB1_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Gallus_gallus_WASHUC2_Ensembl.gtf", "label": "Gallus_gallus_WASHUC2_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Gallus_gallus_build2_1_NCBI.gtf", "label": "Gallus_gallus_build2_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Gallus_gallus_build3_1_NCBI.gtf", "label": "Gallus_gallus_build3_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Gallus_gallus_galGal3_UCSC.gtf", "label": "Gallus_gallus_galGal3_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Gallus_gallus_galGal4_UCSC.gtf", "label": "Gallus_gallus_galGal4_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Glycine_max_Gm01_Ensembl.gtf", "label": "Glycine_max_Gm01_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_GENCODE_hg18_v3c_chr1_format.gtf", "label": "Homo_sapiens_GENCODE_hg18_v3c_chr1_format.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_GENCODE_hg19_v7_1_format.gtf", "label": "Homo_sapiens_GENCODE_hg19_v7_1_format.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf", "label": "Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_GRCh37_Ensembl.gtf", "label": "Homo_sapiens_GRCh37_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_build37_1_NCBI.gtf", "label": "Homo_sapiens_build37_1_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_build37_2_NCBI.gtf", "label": "Homo_sapiens_build37_2_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_hg18_UCSC.gtf", "label": "Homo_sapiens_hg18_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_hg19_UCSC.gtf", "label": "Homo_sapiens_hg19_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Homo_sapiens_hg38_UCSC_GENCODE_v24.gtf", "label": "Homo_sapiens_hg38_UCSC_GENCODE_v24.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Macaca_mulatta_Mmul_1_Ensembl.gtf", "label": "Macaca_mulatta_Mmul_1_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Mus_musculus_GRCm38_Ensembl.gtf", "label": "Mus_musculus_GRCm38_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Mus_musculus_GRCm38_NCBI.gtf", "label": "Mus_musculus_GRCm38_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Mus_musculus_mm10_UCSC.gtf", "label": "Mus_musculus_mm10_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Mus_musculus_mm9_UCSC.gtf", "label": "Mus_musculus_mm9_UCSC.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Oryza_sativa_japonica_MSU6_Ensembl.gtf", "label": "Oryza_sativa_japonica_MSU6_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Plasmodium_falciparum_3D7_v3_Sanger.gtf", "label": "Plasmodium_falciparum_3D7_v3_Sanger.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Rattus_norvegicus_RGSC3_4_Ensembl.gtf", "label": "Rattus_norvegicus_RGSC3_4_Ensembl.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Rattus_norvegicus_RGSC_v3_4_NCBI.gtf", "label": "Rattus_norvegicus_RGSC_v3_4_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Rattus_norvegicus_Rnor_5_0_NCBI.gtf", "label": "Rattus_norvegicus_Rnor_5_0_NCBI.gtf"},
{"url": "https://datasets.genepattern.org/gpftp/module_support_files/annotation/gtf/Saccharomyces_cerevisiae_EF4_Ensembl.gtf", "label": "Saccharomyces_cerevisiae_EF4_Ensembl.gtf"}
]
6 changes: 3 additions & 3 deletions manifest
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Expand Up @@ -45,8 +45,8 @@ p2_value=

p3_MODE=IN
p3_TYPE=FILE
p3_choiceDir=ftp\://gpftp.broadinstitute.org/module_support_files/annotation/gtf/
p3_choiceDirFilter=*.g?f
p3_choiceDir=https://datasets.genepattern.org/gpftp/module_support_files/annotation/index_directory_htseq.json
p3_choiceDirFilter=
p3_default_value=
p3_description=A GTF or GFF file containing a list of gene model annotations. (This file can be gzipped)
p3_fileFormat=gff;gff3;gtf;gtf.gz;gff.gz;gff3.gz
Expand Down Expand Up @@ -218,4 +218,4 @@ quality=preproduction
taskDoc=htseq_count_doc.html
taskType=RNA-seq
userid=bhill@broadinstitute.org
version=Beta release
version=Modified to use datasets.genepattern.org instead of ftp://gpftp.broadinstitutue.org as source for default gtf files

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