{"action":"closed","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1354","repository_url":"https://api.github.com/repos/galaxyproject/tools-iuc","labels_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1354/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1354/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/1354/events","html_url":"https://github.com/galaxyproject/tools-iuc/issues/1354","id":234691885,"node_id":"MDU6SXNzdWUyMzQ2OTE4ODU=","number":1354,"title":"SnpEff Download issues, originally v4.1.0 and still in v4.3k.0","user":{"login":"jennaj","id":8999735,"node_id":"MDQ6VXNlcjg5OTk3MzU=","avatar_url":"https://avatars0.githubusercontent.com/u/8999735?v=4","gravatar_id":"","url":"https://api.github.com/users/jennaj","html_url":"https://github.com/jennaj","followers_url":"https://api.github.com/users/jennaj/followers","following_url":"https://api.github.com/users/jennaj/following{/other_user}","gists_url":"https://api.github.com/users/jennaj/gists{/gist_id}","starred_url":"https://api.github.com/users/jennaj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennaj/subscriptions","organizations_url":"https://api.github.com/users/jennaj/orgs","repos_url":"https://api.github.com/users/jennaj/repos","events_url":"https://api.github.com/users/jennaj/events{/privacy}","received_events_url":"https://api.github.com/users/jennaj/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":27,"created_at":"2017-06-09T00:32:45Z","updated_at":"2018-12-17T23:17:29Z","closed_at":"2018-12-17T23:17:29Z","author_association":"MEMBER","body":"The tool only makes the first genome from a nested .zip available in UI \r\n\r\n**Tool:** SnpEff Download Download a new database (Galaxy Version 4.1.0)\r\n\r\n**Repo:** https://toolshed.g2.bx.psu.edu/repository?repository_id=93a5efea7e957b53&changeset_revision=7adfd0589f49\r\n\r\n**Repo tool version:** 4.3k.0\r\n\r\n_Is an update at http://usegalaxy.org the solution or is the problem still in the newer version of the tool as well or is there some configuration problem?_ \r\n\r\nping @bgruening @davebx @natefoo \r\n\r\n---\r\n**Version 4.1.0 issue**\r\n\r\nThe requested genome is in the list of the available genomes and the stderr for the database download tool _indicates that all of the data is downloaded_. However, only the first genome in the .zip bundle is available through the UI. \r\n\r\nZip archives are not parsed through upload in a default Galaxy (nor at Galaxy Main). Only the first file is loaded. Not sure if related but seemed worth mentioning.\r\n\r\nhttps://usegalaxy.org/u/jen/h/snpeff-database-download-test-history\r\n\r\n<img width=\"970\" alt=\"screen shot 2017-06-08 at 4 40 58 pm\" src=\"https://user-images.githubusercontent.com/8999735/26955562-5aca7866-4c6c-11e7-92e2-c7e7cf682bf1.png\">\r\n\r\n**Genome requested by the tool:**\r\n\r\nhttps://www.ncbi.nlm.nih.gov/genome/?term=txid264462[Organism:noexp]\r\n**Bdellovibrio_bacteriovorus_HD100_uid61595**\r\nrefseq: NC_005363.1\r\nINSDC: BX842601.2\r\n\r\n**Genome accessible by SnpEff tool:**\r\n\r\nhttps://www.ncbi.nlm.nih.gov/genome/486?genome_assembly_id=167053\r\n**Bacillus_thuringiensis_BMB171_uid49135**\r\nchr refseq: NC_014171.1\t\r\nchr INSDC: CP001903.1\r\nplsm refseq: NC_014172.1\r\nplsm INSDC: CP001904.1\r\n\r\nExamining the target .zip when obtained directly (using the same path that the tool uses) shows that the zip does have the target genome in the set. The genome available through the UI is the first in the archive.\r\n\r\n> $ curl https://managedway.dl.sourceforge.net/project/snpeff/databases/v4_1/snpEff_v4_1_NCBI_bacterial_4.zip > snpEff_v4_1_NCBI_bacterial_4.zip\r\n>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n>                                  Dload  Upload   Total   Spent    Left  Speed\r\n> 100  102M  100  102M    0     0  5530k      0  0:00:18  0:00:18 --:--:-- 5725k\r\n> $ unzip snpEff_v4_1_NCBI_bacterial_4.zip\r\n> Archive:  snpEff_v4_1_NCBI_bacterial_4.zip\r\n>   inflating: wsu/home/eq/eq83/eq8302/snpEff/data/Bacillus_thuringiensis_BMB171_uid49135/snpEffectPredictor.bin  \r\n>   inflating: wsu/home/eq/eq83/eq8302/snpEff/data/Bacillus_thuringiensis_Bt407_uid177931/snpEffectPredictor.bin\r\n>   inflating: wsu/home/eq/eq83/eq8302/snpEff/data/Bacillus_thuringiensis_HD_771_uid173374/snpEffectPredictor.bin\r\n> etc.. for all \r\n\r\n> $ ls\r\n> Bacillus_thuringiensis_BMB171_uid49135\r\n> Bacillus_thuringiensis_Bt407_uid177931\r\n> Bacillus_thuringiensis_HD_771_uid173374\r\n> Bacillus_thuringiensis_HD_789_uid173860\r\n> Bacillus_thuringiensis_MC28_uid176369\r\n> Bacillus_thuringiensis_YBT_1518_uid229419\r\n> Bacillus_thuringiensis_serovar_IS5056_uid190186\r\n> Bacillus_thuringiensis_serovar_chinensis_CT_43_uid158151\r\n> Bacillus_thuringiensis_serovar_finitimus_YBT_020_uid158875\r\n> Bacillus_thuringiensis_serovar_konkukian_97_27_uid58089\r\n> Bacillus_thuringiensis_serovar_kurstaki_HD73_uid189188\r\n> Bacillus_toyonensis_BCT_7112_uid227218\r\n> Bacillus_weihenstephanensis_KBAB4_uid58315\r\n> Bacteriovorax_marinus_SJ_uid82341\r\n> Bacteroides_CF50_uid222805\r\n> Bacteroides_fragilis_638R_uid84217\r\n> Bacteroides_fragilis_NCTC_9343_uid57639\r\n> Bacteroides_fragilis_YCH46_uid58195\r\n> Bacteroides_helcogenes_P_36_108_uid62135\r\n> Bacteroides_salanitronis_DSM_18170_uid63269\r\n> Bacteroides_thetaiotaomicron_VPI_5482_uid62913\r\n> Bacteroides_uniformis_uid13130\r\n> Bacteroides_vulgatus_ATCC_8482_uid58253\r\n> Bacteroides_xylanisolvens_XB1A_uid197168\r\n> Bartonella_australis_Aust_NH1_uid189950\r\n> Bartonella_bacilliformis_KC583_uid58533\r\n> Bartonella_clarridgeiae_73_uid62131\r\n> Bartonella_grahamii_as4aup_uid59405\r\n> Bartonella_henselae_Houston_1_uid57745\r\n> Bartonella_quintana_RM_11_uid174512\r\n> Bartonella_quintana_Toulouse_uid57635\r\n> Bartonella_tribocorum_CIP_105476_uid59129\r\n> Bartonella_vinsonii_berkhoffii_Winnie_uid189951\r\n> Baumannia_cicadellinicola_Hc__Homalodisca_coagulata__uid58111\r\n> Bdellovibrio_bacteriovorus_HD100_uid61595\r\n> Bdellovibrio_bacteriovorus_Tiberius_uid182482\r\n> Bdellovibrio_exovorus_JSS_uid194119\r\n> Beijerinckia_indica_ATCC_9039_uid59057\r\n> Belliella_baltica_DSM_15883_uid168182\r\n> Beutenbergia_cavernae_DSM_12333_uid59047\r\n> Bibersteinia_trehalosi_192_uid193709\r\n> Bifidobacterium_adolescentis_ATCC_15703_uid58559\r\n> Bifidobacterium_animalis_ATCC_25527_uid162513\r\n> Bifidobacterium_animalis_lactis_AD011_uid58911\r\n> Bifidobacterium_animalis_lactis_ATCC_27673_uid222803\r\n> Bifidobacterium_animalis_lactis_B420_uid163691\r\n> Bifidobacterium_animalis_lactis_BB_12_uid158871\r\n> Bifidobacterium_animalis_lactis_BLC1_uid158867\r\n> Bifidobacterium_animalis_lactis_Bi_07_uid163693\r\n> Bifidobacterium_animalis_lactis_Bl12_uid210081\r\n> Bifidobacterium_animalis_lactis_Bl_04_uid59359\r\n> Bifidobacterium_animalis_lactis_CNCM_I_2494_uid158869\r\n> Bifidobacterium_animalis_lactis_DSM_10140_uid59357\r\n> Bifidobacterium_animalis_lactis_V9_uid158865\r\n> Bifidobacterium_asteroides_PRL2011_uid176921\r\n> Bifidobacterium_bifidum_BGN4_uid167988\r\n> Bifidobacterium_bifidum_PRL2010_uid59883\r\n> Bifidobacterium_bifidum_S17_uid59545\r\n> Bifidobacterium_breve_ACS_071_V_Sch8b_uid158863\r\n> Bifidobacterium_breve_UCC2003_uid193702\r\n> Bifidobacterium_dentium_Bd1_uid43091\r\n> Bifidobacterium_longum_BBMN68_uid60163\r\n> Bifidobacterium_longum_DJO10A_uid58833\r\n> Bifidobacterium_longum_F8_uid197184\r\n> Bifidobacterium_longum_JCM_1217_uid62695\r\n> Bifidobacterium_longum_JDM301_uid49131\r\n> Bifidobacterium_longum_KACC_91563_uid158861\r\n> Bifidobacterium_longum_NCC2705_uid57939\r\n> Bifidobacterium_longum_infantis_157F_uid62693\r\n> Bifidobacterium_longum_infantis_ATCC_15697_uid159865\r\n> Bifidobacterium_longum_infantis_ATCC_15697_uid58677\r\n> Bifidobacterium_thermophilum_RBL67_uid193770\r\n> Blastococcus_saxobsidens_DD2_uid89391\r\n> Blattabacterium__Blaberus_giganteus__uid165873\r\n> Blattabacterium__Blatta_orientalis__Tarazona_uid188115\r\n> Blattabacterium__Blattella_germanica__Bge_uid41533\r\n> Blattabacterium__Cryptocercus_punctulatus__Cpu_uid81083\r\n> Blattabacterium__Mastotermes_darwiniensis__MADAR_uid77127\r\n> Blattabacterium__Nauphoeta_cinerea__uid222815\r\n> Blattabacterium__Panesthia_angustipennis_spadica__BPAA_uid193717\r\n> Blattabacterium__Periplaneta_americana__BPLAN_uid41287\r\n> Bordetella_avium_197N_uid61563\r\n> Bordetella_bronchiseptica_253_uid178913\r\n> Bordetella_bronchiseptica_MO149_uid177517\r\n> Bordetella_bronchiseptica_RB50_uid57613\r\n> Bordetella_parapertussis_12822_uid57615\r\n> Bordetella_parapertussis_18323_uid175569\r\n> Bordetella_parapertussis_Bpp5_uid177516\r\n> Bordetella_pertussis_CS_uid158859\r\n> Bordetella_pertussis_Tohama_I_uid57617\r\n> Bordetella_petrii_uid61631\r\n> Borrelia_afzelii_HLJ01_uid177930\r\n> Borrelia_afzelii_PKo_uid159867\r\n> Borrelia_afzelii_PKo_uid58653\r\n> Borrelia_bissettii_DN127_uid71231\r\n> Borrelia_burgdorferi_B31_uid57581\r\n> Borrelia_burgdorferi_CA382_uid214794\r\n> Borrelia_burgdorferi_JD1_uid161197\r\n> Borrelia_burgdorferi_N40_uid161241\r\n> Borrelia_burgdorferi_ZS7_uid59429\r\n> Borrelia_crocidurae_Achema_uid162335\r\n> Borrelia_duttonii_Ly_uid58791\r\n> Borrelia_garinii_BgVir_uid162165\r\n> Borrelia_garinii_NMJW1_uid177081\r\n> Borrelia_garinii_PBi_uid58125\r\n> Borrelia_hermsii_DAH_uid59225\r\n> Borrelia_miyamotoi_LB_2001_uid215233\r\n> Borrelia_recurrentis_A1_uid58793\r\n> bacterium_BT_1_uid184079\r\n> beta_proteobacterium_CB_uid191340\r\n\r\n\r\n\r\n\r\n\r\n"}}
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