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glassgo_wrapper.xml |
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._README.rst ._accession_lists_links.txt ._glassgo_macros.xml ._glassgo_wrapper.xml ._test-data README.rst accession_lists_links.txt config_lookup/._.DS_Store config_lookup/._config_lookup.py config_lookup/config_lookup.py config_lookup/dist/config_lookup glassgo_macros.xml test-data/._NsiR4_Synechocystis_sp_PCC6803.fa test-data/._glassgo_NsiR4_Synechocystis_sp_PCC6803.fa test-data/NsiR4_Synechocystis_sp_PCC6803.fa test-data/glassgo_NsiR4_Synechocystis_sp_PCC6803.fa tool-data/._.DS_Store tool-data/._glassgo_accession_list.txt tool-data/glassgo_accession_list.txt |
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| diff -r a127bf2287b9 -r 76b7a84ba942 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jan 14 06:03:45 2020 -0500 |
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| @@ -0,0 +1,42 @@ +Configuration of Galaxy to run GLASSgo in Docker +================================================ + +Prerequisites +------------- + +1) configure Galaxy to run tools in Docker as described at \ + https://galaxyproject.org/admin/tools/docker/. In addition, GLASSgo requires the current BLAST nucleotide database. For that, the `tool-data/blastdb.loc` has to be configured accordingly as the GLASSgo wrapper reads this information as options when laying out the user interface. We use Docker volumes to do so (Docker CLI option -v). + For that, we add Docker volumes to the (id=`docker_local`) Docker destination + + `<param id="docker_volumes">$defaults,/Volumes/TC1/nt:/Volumes/TC1/nt/</param>` + + More information can be found in the ./config/job_conf.xml.sample_advanced (https://github.com/galaxyproject/galaxy/blob/release_18.09/config/job_conf.xml.sample_advanced#L378) of any Galaxy instance. Obviously, the exposed folder needs to be identical with the path specified in `tool-data/blastdb.loc`. Here the local folder `Volumes/TC1/nt` contains the BLAST database and is exposed to the Docker container. In this case, the folder is bound to the same location in the container. This allows to execute the GLASSgo call in the tool XML file directly with the selected option. + +2) Install GLASSgo from the Galaxy Toolshed + (https://toolshed.g2.bx.psu.edu/view/computationaltranscriptomics/glassgo). + Afterwards, the Galaxy instance needs to be configured such that it is aware of the accession lists. This can be done either manually or using a custom script. + + - download the accession lists from Zenodo (https://zenodo.org/record/1320180) and copy the file `glassgo_accession_list.txt` (./tool-data/glassgo_accession_list.txt) into the folder `tool-data` of Galaxy (e.g., `/galaxy/tool-data/`) or + + - use `config_lookup` (./config_lookup/dist/) to download the look tables using `accession_lists_links.txt`(./accession_lists_links.txt) + (option --acclinks) and creates `glassgo_accession_list.txt` in `tool-data` of Galaxy. + + Note: Any changes of files within `tool-data` requires a (re)start of Galaxy. + + +config_lookup +------------- +` +usage: config_lookup [-h] --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS] + +incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches + +optional arguments: + -h, --help show this help message and exit + --galaxy GALAXY (absolute) path to the root directory of the Galaxy instance + --acclinks ACCLINKS (absolute) path to file containing URLs to the accession lists + --acclists ACCLISTS (absolute) path to directory to save the accession lists to +` + + + |
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| @@ -0,0 +1,29 @@ +https://zenodo.org/record/1320180/files/Alphaproteobacteria.acc +https://zenodo.org/record/1320180/files/Aquificae.acc +https://zenodo.org/record/1320180/files/Archaea.acc +https://zenodo.org/record/1320180/files/Armatimonadetes.acc +https://zenodo.org/record/1320180/files/Bacteria.acc +https://zenodo.org/record/1320180/files/Bacteroidetes.acc +https://zenodo.org/record/1320180/files/Caldiserica.acc +https://zenodo.org/record/1320180/files/Chlamydiae.acc +https://zenodo.org/record/1320180/files/Chloroflexi.acc +https://zenodo.org/record/1320180/files/Chrysiogenetes.acc +https://zenodo.org/record/1320180/files/Cyanobacteria.acc +https://zenodo.org/record/1320180/files/Deferribacteres.acc +https://zenodo.org/record/1320180/files/Deinococcus-thermus.acc +https://zenodo.org/record/1320180/files/Dictyoglomi.acc +https://zenodo.org/record/1320180/files/Elusimicrobia.acc +https://zenodo.org/record/1320180/files/Fibrobacteres.acc +https://zenodo.org/record/1320180/files/Firmicutes.acc +https://zenodo.org/record/1320180/files/Fusobacteria.acc +https://zenodo.org/record/1320180/files/Gemmatimonadetes.acc +https://zenodo.org/record/1320180/files/Nitrospinae.acc +https://zenodo.org/record/1320180/files/Nitrospirae.acc +https://zenodo.org/record/1320180/files/Planctomycetes.acc +https://zenodo.org/record/1320180/files/Proteobacteria.acc +https://zenodo.org/record/1320180/files/Spirochaetes.acc +https://zenodo.org/record/1320180/files/Synergistetes.acc +https://zenodo.org/record/1320180/files/Tenericutes.acc +https://zenodo.org/record/1320180/files/Thermodesulfobacteria.acc +https://zenodo.org/record/1320180/files/Thermotogae.acc +https://zenodo.org/record/1320180/files/Viruses.acc |
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| @@ -0,0 +1,75 @@ +#!/usr/local/bin/python3 + +''' +This script downloads lookup tables and integrates these into the Galaxy instance + +USAGE + config_lookup.py --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS] + +OPTIONS + -h, --help show this help message and exit + +''' + +import os +import argparse +import requests +import sys +import shutil + + +def main(): + # parse arguments + parser = argparse.ArgumentParser(description='incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches') + parser.add_argument('--galaxy', required=True, help='(absolute) path to the root directory of the Galaxy instance') + parser.add_argument('--acclinks', required=True, help='(absolute) path to file containing URLs to the accession lists') + parser.add_argument('--acclists', help='(absolute) path to directory to save the accession lists to') + args = parser.parse_args() + + # ./acclists as default folder for the accession lists + if args.acclists == None: + args.acclists = os.path.join(os.getcwd(),'acclists') + + # check for existence of the folders for galaxy and URLs to the accession lists + if not os.path.exists(args.galaxy): + print('\tERROR: ' + args.galaxy + ' could not be found!') + sys.exit() + if not os.path.exists(args.acclinks): + print('\tERROR: ' + args.acclinks + ' could not be found!') + sys.exit() + + print('################ configure the accession lists ################') + print('### the accession lists will be saved to ' + args.acclists) + + # create folder for accession lists + if not os.path.exists(args.acclists): + os.makedirs(args.acclists) + + # + with open(args.acclinks, 'r') as link: + # create list with lookup tables that populates the user interface + accDataTableFile = os.path.join(os.getcwd(),'tool-data/glassgo_accession_list.txt') + + accDataTable = open(accDataTableFile,'w') + accDataTable.write('global\tglobal\n') + # fetch accession lists + for url in link: + acc = requests.get(url) + filename = str(os.path.basename(url)).replace('\n','') + print('### fetch: ' + filename) + open(os.path.join(args.acclists,filename),'wb').write(acc.content) + + # + accDataTable.write(filename + '\t') + accDataTable.write(os.path.join(args.acclists,filename) + '\n') + + accDataTable.close() + print('### create tab-separated list '+ accDataTableFile) + + # move list with accession list to /galaxy/tool-data + shutil.copy(accDataTableFile,os.path.join(args.galaxy,'tool-data/')) + print('### move tab-separated list to ' + str(os.path.join(args.galaxy,'tool-data/'))) + +# +if __name__ == "__main__": + main() |
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| @@ -0,0 +1,8 @@ +<macros> + <token name="@VERSION@">1.5.2</token> + <xml name="requirements"> + <requirements> + <container type="docker">lotts/glassgo_acc_version:latest</container> + </requirements> + </xml> +</macros> \ No newline at end of file |
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| diff -r a127bf2287b9 -r 76b7a84ba942 glassgo_wrapper.xml --- a/glassgo_wrapper.xml Tue Jan 14 05:57:28 2020 -0500 +++ b/glassgo_wrapper.xml Tue Jan 14 06:03:45 2020 -0500 |
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| @@ -15,9 +15,9 @@ -p ${search.cond_param_setup.identity} #end if -u ${additional_setting.upstream_region} - #if str($search.cond_taxon_setup.taxon_setup) == "acclist": - -g ${search.cond_taxon_setup.acclist} - #end if + #if str($search.acclist) != "global": + -g ${search.acclist} + #end if -n 500 -o $output ]]> @@ -29,20 +29,16 @@ <options from_file="blastdb.loc"> <column name="name" index="1"/> <column name="value" index="2"/> - <filter type="regexp" value="nt_.*" column="0" /> </options> </param> </section> <section name="search" title="Search Parameters" expanded="true"> - <conditional name="cond_taxon_setup"> - <param name="taxon_setup" type="select" label="Taxon Selection"> - <option value="global">global search</option> - <option value="acc">accession list from user history</option> - </param> - <when value="acc"> - <param name="acclist" type="data" format="txt" label="Accession List" /> - </when> - </conditional> + <param name="acclist" type="select" label="Choose taxon"> + <options from_file="glassgo_accession_list.txt"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> <conditional name="cond_param_setup"> <param name="param_setup" type="select" display="radio" label="Parameter Setup"> <option value="automatic">automatic</option> @@ -117,6 +113,8 @@ The GLASSgo search is by default based on the complete NCBI Nucleotide database. In general, sRNAs show a limited distribution among the phylogenetic tree, such that a targeted search in a specfic taxonomic group is likely to perform better. For that, we provide accession lists for the taxonomic groups the search should be limited to. + + - **Parameter Setup** You can run GLASSgo either in automated mode or you can manually set the advanced parameters. |
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| @@ -0,0 +1,2 @@ +>NsiR4_Synechocystis_sp_PCC6803 +AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT \ No newline at end of file |
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| diff -r a127bf2287b9 -r 76b7a84ba942 test-data/glassgo_NsiR4_Synechocystis_sp_PCC6803.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glassgo_NsiR4_Synechocystis_sp_PCC6803.fa Tue Jan 14 06:03:45 2020 -0500 |
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| b'@@ -0,0 +1,144 @@\n+>NsiR4_Synechocystis_sp_PCC6803\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>CP017708.1:6970845-6970912 Moorea producens JHB sequence-p.c.VAL:60.47%-taxID:1454205\n+ACCAAGTAACCTAGAGTTACCCTCCGATTGCTTAACCATGCCGCCCTATTGCTAGCGGCGGTTTTTTA\n+>CP011304.1:c510694-510626 Microcystis aeruginosa NIES-2549, complete genome-p.c.VAL:61.63%-taxID:1641812\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAGAAAATGTTTGGATCGCTTAATATTTAAGCCC\n+>CP024785.1:c5901670-5901600 Nostoc flagelliforme CCNUN1 chromosome, complete genome-p.c.VAL:60.23%-taxID:2038116\n+GCAGAGTAATCTGTAATTACCCTCCGATTGCTTAACCAAACCGCCCTATGATATTTAGTGGCGGTTTTTTT\n+>AP017295.1:c5126310-5126244 Nostoc sp. NIES-3756 DNA, complete genome-p.c.VAL:61.18%-taxID:1751286\n+CGAAGTAGGCTATAGATTACCCTCCGATTGCTTAACCAGACCGCCCTAACCTAGTGGCGGTTTTTTT\n+>CP012375.1:c508130-508062 Microcystis aeruginosa NIES-2481, complete genome-p.c.VAL:61.63%-taxID:1698524\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAGAAAATGTTTGGATCGCTTAATATTTAAGCCC\n+>AP018248.1:c2285028-2284962 Tolypothrix tenuis PCC 7101 DNA, nearly complete genome-p.c.VAL:55.68%-taxID:231146\n+GCAATTTAAGCTATAAATACCCTCCGATTGCTTAACCAAACCGCCCTAGATTAGCGGCGGTTTCCTC\n+>CP003653.1:c4488913-4488847 Stanieria cyanosphaera PCC 7437, complete genome-p.c.VAL:61.18%-taxID:111780\n+AAAGCTTAAGCTATTATTACCCTCCGATTGCTTATTCAGACCGCCCAAATCTAGAGGCGGTTTTTTA\n+>AP012205.1:c1288143-1288074 Synechocystis sp. PCC 6803 DNA, complete genome, strain: GT-S-p.c.VAL:100.0%-taxID:1148\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>AP012277.1:c1288386-1288317 Synechocystis sp. PCC 6803 substr. PCC-N DNA, complete genome-p.c.VAL:100.0%-taxID:1080229\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>AP018174.1:1782280-1782351 Anabaenopsis circularis NIES-21 DNA, nearly complete genome-p.c.VAL:59.55%-taxID:1085406\n+CCCAGAGTAATCTTTAATTACCCTCCGATTGCTTAACCAGACAACCGCCATAATTTAGTGGCGGTTTTTTAT\n+>CP020771.1:c600281-600213 Microcystis aeruginosa PCC 7806SL chromosome, complete genome-p.c.VAL:63.53%-taxID:1903187\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAGAAAATGTTTGAATCGCTTAATATTTGGGCTT\n+>AP012278.1:c1288398-1288329 Synechocystis sp. PCC 6803 substr. PCC-P DNA, complete genome-p.c.VAL:100.0%-taxID:1080230\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>CP007542.1:c257489-257420 Synechocystis sp. PCC 6714, complete genome-p.c.VAL:97.18%-taxID:1147\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCGTTGCTTCAGTGGCGGCTTTCTTTTT\n+>AP018207.1:4141752-4141819 Calothrix brevissima NIES-22 DNA, nearly complete genome-p.c.VAL:58.62%-taxID:1973478\n+TCAAGAGTAATCTATATCTACCCTCCGATTGCTTAACTAAACCGCCCTCGTTTTGCGGCGGTTTTCTC\n+>AP018318.1:c3470288-3470217 Nostoc sp. HK-01 DNA, complete genome-p.c.VAL:59.55%-taxID:196308\n+CCCAGAGTAATCTTTAATTACCCTCCGATTGCTTAACCAGACAACCGCCATAATTTAGTGGCGGTTTTTTAT\n+>AP018269.1:749499-749565 Cylindrospermum sp. NIES-4074 DNA, nearly complete genome-p.c.VAL:61.18%-taxID:2005457\n+AGCATAGTAAGCTAAAACTACCCTCCGATTACTTAACCACACCGCCCTCATTTAGTGGCGGTTTTTT\n+>CP011339.1:2880774-2880842 Microcystis panniformis FACHB-1757, complete genome-p.c.VAL:63.53%-taxID:1638788\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAAAAAATGTTTGGATCGCTTAGTATTTAAGCCT\n+>AP018172.1:7286537-7286603 Calothrix sp. NIES-2098 DNA, complete genome-p.c.VAL:57.47%-taxID:1954171\n+GCAGAGTAAGCTATAACTACCCTCCGATTGCTTAACCAGACCGCCCTAGTTTAGCGGCGGTTTTCTC\n+>BA000019.2:c4499343-4499277 Nostoc sp. PCC 7120 DNA, complete genome-p.c.VAL:63.1%-taxID:103690\n+CAGAATAGGCTAGAGATTACCCTCCGATTGCTTAACCAGACCGCCCTAATCTAGTGGCGGTTTTTTT\n+>AP019314.1:2189722-2189790 Microcystis viridis NIES-102 DNA, complete genome-p.c.VAL:61.63%-taxID:213615\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAAAAAATGTTTGGATCGCTTAAGGTTTAAGCCT\n+>AP018178.1:6725304-6725371 Calothrix sp. NIES-2100 DNA, nearly complete genome-p.c.VAL:62.35%-taxID:1954172\n+TAAAGAGTAAGCTATATCTACCCTCCGATTGCTTAACTAGACCGCCCTTGTTTAGCGGCGGTTTTCTC\n+>AP012276.1:c1288245-1288176 Synechocystis sp. PCC 6803 substr. GT-I DNA, complete genome-p.c.VAL:10'..b"+>CP011382.1:c4400583-4400515 Calothrix sp. 336/3, complete genome-p.c.VAL:65.48%-taxID:1337936\n+CCAGAGTAATCTGTAAATACCCTCCGATTGCTTAACCAGACCGCCCTACTTCTCAGTGGCGGTTTTTTT\n+>AP018194.1:c3394929-3394863 Scytonema sp. HK-05 DNA, nearly complete genome-p.c.VAL:63.1%-taxID:1137095\n+GCACAGTAAGCTATAAATACCCTCCGATTGCTTAACCAGACCGCCCTAATTAAGTGGCGGTTTTTTT\n+>AP009552.1:4321642-4321710 Microcystis aeruginosa NIES-843 DNA, complete genome-p.c.VAL:61.63%-taxID:449447\n+AAGACATAAAGTCAATATCACCCTCCGATTGCAATGAAAAAATGTTTGGATCGCTTAAGGTTTAAGCCT\n+>CP026681.1:1035105-1035175 Nostoc sp. 'Peltigera membranacea cyanobiont' N6 chromosome, complete genome-p.c.VAL:63.95%-taxID:1261031\n+GCAGAGTAATCTGTAATTACCCTCCGATTGCTTAACCAGACCGCCCTATTATACTTAGTGGCGGTTTTTTT\n+>CP028094.1:c1288143-1288074 Synechocystis sp. IPPAS B-1465 chromosome, complete genome-p.c.VAL:100.0%-taxID:2116702\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>CP040360.1:2869162-2869235 Synechococcus sp. PCC 11901 chromosome, complete genome-p.c.VAL:56.52%-taxID:2579791\n+CCCGCGCTAGGTTAGCAATACCCTCCGATTGCTTATCAAGCTAGACCGTCCTCACCCAGTGGCGGTTTTTTATT\n+>CP012832.1:c1288399-1288330 Synechocystis sp. PCC 6803 substrain GT-G, complete genome-p.c.VAL:100.0%-taxID:1148\n+AAGACATAAAGTCAATATCACCCTCCGATTGCTAGAGGTCGCCCATTGCTTCAGTGGCGGCTTTCTTTTT\n+>CP000117.1:4424793-4424859 Anabaena variabilis ATCC 29413, complete genome-p.c.VAL:65.06%-taxID:240292\n+CAGAATAGGCTAGATATTACCCTCCGATTGCTTAACCAGACCGCCCTAATCTAGTGGCGGTTTTTTT\n+>AP012549.1:5724-5792 Cyanobacterium endosymbiont of Epithemia turgida isolate EtSB Lake Yunoko DNA, complete genome-p.c.VAL:63.53%-taxID:1228987\n+AATACATAAAGTCAATTATTAGCCTTCGATTGCTTAGGATGACTACTCACTCTTTAGTGGTATTTTTTC\n+>AF381044.1:400-473 Synechococcus sp. PCC 7002 type II NADH dehydrogenase B (ndbB) gene, complete cds-p.c.VAL:56.52%-taxID:32049\n+CCCGCGCTAGGTTAGCAATACCCTCCGATTGCTTATCAAGCTAGACCGTCCTCACCCAGTGGCGGTTTTTTATT\n+>CP003620.1:3331800-3331870 Crinalium epipsammum PCC 9333, complete genome-p.c.VAL:67.86%-taxID:1173022\n+AGCAACGTAAGGTATTGATACCCTCCGATTGCTTAAGACGACCGCCCTCTTTCTAGTGGCGGTTTTTTATT\n+>CP003642.1:c4145251-4145185 Cylindrospermum stagnale PCC 7417, complete genome-p.c.VAL:59.3%-taxID:56107\n+GCAAAGTAAACTGTAAGTACCCTCCGATTGCTTAACCAAACCGCCCTCATCTTGTGGCGGTTTTTTC\n+>CP002059.1:2779593-2779658 'Nostoc azollae' 0708, complete genome-p.c.VAL:61.9%-taxID:551115\n+AATTAAGTAAGGTGTAATTACCCTCCGATTGCTTAAGCATACCGCCCCCACTAGAGGCGGTTTTTT\n+>AP018290.1:9037675-9037744 Calothrix sp. NIES-4105 DNA, nearly complete genome-p.c.VAL:60.92%-taxID:2005463\n+GCAGAGTAAGCTATTAATACCCTCCGATTGCTTAACCAGACCGCCCATTTAATTTTAGGGCGGTTTTTTT\n+>CP016477.1:2215408-2215481 Synechococcus sp. PCC 7117, complete genome-p.c.VAL:56.52%-taxID:195498\n+CCCGCGCTAGGTTAGCAATACCCTCCGATTGCTTATCAAGCTAGACCGTCCTCACCCAGTGGCGGTTTTTTATT\n+>CP003549.1:c1417649-1417583 Rivularia sp. PCC 7116, complete genome-p.c.VAL:65.06%-taxID:373994\n+GCAGAGTAACCTATAAATACCCTCCGATTGCTTAACCAGACCGCCCTATTTTAGTGGCGGTTTTTTT\n+>CP003610.1:c5163331-5163265 Calothrix sp. PCC 6303, complete genome-p.c.VAL:65.06%-taxID:1170562\n+GTAGACTAAGCTAATCATACCCTCCGATTGCTTAACCAGACCGCCCTTATCTAGAGGCGGTTTTTTT\n+>AP018227.1:c6677631-6677565 Calothrix parasitica NIES-267 DNA, nearly complete genome-p.c.VAL:63.1%-taxID:1973488\n+AGCAGAGTAATGTGTAAATACCCTCCGATTGCTTAACCAAACCGCCCTATTTTAGTGGCGGTTTTTT\n+>AP017305.1:c2087972-2087903 Fischerella sp. NIES-3754 DNA, complete genome-p.c.VAL:64.71%-taxID:1752063\n+GCACAGTAAGCTGAAAATACCCTCCGATTGCTTAACCAGACCGCCCTACTCTACTAGTGGCGGTTTTTTT\n+>AP018307.1:113675-113741 Aulosira laxa NIES-50 DNA, nearly complete genome-p.c.VAL:55.68%-taxID:1541988\n+GCAATTTAAGCTATAAATACCCTCCGATTGCTTAACCAAACCGCCCTAGATTAGCGGCGGTTTCCTC\n+>CP013998.1:2202505-2202578 Synechococcus sp. PCC 73109, complete genome-p.c.VAL:56.52%-taxID:374982\n+CCCGCGCTAGGTTAGCAATACCCTCCGATTGCTTATCAAGCTAGACCGTCCTCACCCAGTGGCGGTTTTTTATT\n+>AP018184.1:1339916-1339982 Nostoc sp. NIES-2111 DNA, nearly complete genome-p.c.VAL:61.18%-taxID:1973475\n+CGAAGTAGGCTATAGATTACCCTCCGATTGCTTAACCAGACCGCCCTAACCTAGTGGCGGTTTTTTT\n" |
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| Binary file tool-data/._.DS_Store has changed |
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| diff -r a127bf2287b9 -r 76b7a84ba942 tool-data/._glassgo_accession_list.txt |
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| Binary file tool-data/._glassgo_accession_list.txt has changed |
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| diff -r a127bf2287b9 -r 76b7a84ba942 tool-data/glassgo_accession_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/glassgo_accession_list.txt Tue Jan 14 06:03:45 2020 -0500 |
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| @@ -0,0 +1,30 @@ +global global +Alphaproteobacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Alphaproteobacteria.acc +Aquificae.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Aquificae.acc +Archaea.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Archaea.acc +Armatimonadetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Armatimonadetes.acc +Bacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Bacteria.acc +Bacteroidetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Bacteroidetes.acc +Caldiserica.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Caldiserica.acc +Chlamydiae.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Chlamydiae.acc +Chloroflexi.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Chloroflexi.acc +Chrysiogenetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Chrysiogenetes.acc +Cyanobacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Cyanobacteria.acc +Deferribacteres.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Deferribacteres.acc +Deinococcus-thermus.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Deinococcus-thermus.acc +Dictyoglomi.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Dictyoglomi.acc +Elusimicrobia.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Elusimicrobia.acc +Fibrobacteres.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Fibrobacteres.acc +Firmicutes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Firmicutes.acc +Fusobacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Fusobacteria.acc +Gemmatimonadetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Gemmatimonadetes.acc +Nitrospinae.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Nitrospinae.acc +Nitrospirae.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Nitrospirae.acc +Planctomycetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Planctomycetes.acc +Proteobacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Proteobacteria.acc +Spirochaetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Spirochaetes.acc +Synergistetes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Synergistetes.acc +Tenericutes.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Tenericutes.acc +Thermodesulfobacteria.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Thermodesulfobacteria.acc +Thermotogae.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Thermotogae.acc +Viruses.acc /Users/riasc/Documents/galaxy/tools/docker/glassgo/acclists/Viruses.acc |