From c8c547111dba87030242b1f67d1d39d351b1e562 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 27 May 2020 19:22:29 -0700 Subject: [PATCH 1/5] Specify minimum Galaxy version of 18.09 for data managers Tools of tool_type="manage_data" with a profile < 18.09 are loaded in legacy mode by Galaxy. Legacy mode preserves Galaxies python environment while activating the mentalist conda environment. This causes the tools to use the incorrect version of python. --- .../data_manager/mentalist_build_db.xml | 2 +- .../data_manager/mentalist_download_cgmlst.xml | 2 +- .../data_manager/mentalist_download_enterobase.xml | 2 +- .../data_manager/mentalist_download_pubmlst.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml b/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml index 772e30c..0006432 100644 --- a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml +++ b/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml @@ -1,5 +1,5 @@ - + mentalist diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml index 71fa0ed..3166ac1 100644 --- a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml +++ b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml @@ -1,5 +1,5 @@ - + mentalist diff --git a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml b/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml index a27cdc5..5fcee83 100644 --- a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml +++ b/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml @@ -1,5 +1,5 @@ - + mentalist diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml index ccc8107..4562897 100644 --- a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml +++ b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml @@ -1,5 +1,5 @@ - + mentalist From 4c6c938f8f3b83b1d1d165fef3e116678e18f0e8 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Mon, 22 Jun 2020 09:59:31 -0700 Subject: [PATCH 2/5] Refactor data managers, eliminating extraneous python dependency in place of jq Deduplicate data manager tools into single tool Replace hard coded database list for output of mentalist list commands Bump mentalist version to 0.2.5 --- Manifest.toml | 366 ++++++++++++++++++ README.md | 2 + conda/build.sh | 12 - conda/meta.yaml | 36 -- galaxy/data_manager_conf.xml | 29 ++ galaxy/data_managers/data_manager_conf.xml | 63 --- .../data_manager_mentalist_build_db/.shed.yml | 10 - .../data_manager/mentalist_build_db.py | 67 ---- .../data_manager/mentalist_build_db.xml | 36 -- .../tool_data_table_conf.xml.sample | 8 - .../.shed.yml | 10 - .../data_manager/mentalist_download_cgmlst.py | 73 ---- .../mentalist_download_cgmlst.xml | 37 -- .../tool-data/mentalist_databases.loc.sample | 0 .../tool_data_table_conf.xml.sample | 8 - .../.shed.yml | 11 - .../mentalist_download_enterobase.py | 79 ---- .../mentalist_download_enterobase.xml | 35 -- .../tool_data_table_conf.xml.sample | 8 - .../.shed.yml | 11 - .../mentalist_download_pubmlst.py | 74 ---- .../mentalist_download_pubmlst.xml | 161 -------- .../tool-data/mentalist_databases.loc.sample | 0 .../tool_data_table_conf.xml.sample | 8 - galaxy/enterobase.tsv | 4 + .../mentalist_call => }/mentalist_call.xml | 7 +- .../mentalist_databases.loc.sample | 0 galaxy/mentalist_download.xml | 100 +++++ galaxy/tool_data_table_conf.xml.sample | 12 + galaxy/tsvs_to_galaxy | 10 + 30 files changed, 526 insertions(+), 751 deletions(-) create mode 100644 Manifest.toml delete mode 100644 conda/build.sh delete mode 100644 conda/meta.yaml create mode 100644 galaxy/data_manager_conf.xml delete mode 100644 galaxy/data_managers/data_manager_conf.xml delete mode 100644 galaxy/data_managers/data_manager_mentalist_build_db/.shed.yml delete mode 100644 galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py delete mode 100644 galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml delete mode 100644 galaxy/data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_cgmlst/.shed.yml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool-data/mentalist_databases.loc.sample delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_enterobase/.shed.yml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_pubmlst/.shed.yml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool-data/mentalist_databases.loc.sample delete mode 100644 galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample create mode 100644 galaxy/enterobase.tsv rename galaxy/{tools/mentalist_call => }/mentalist_call.xml (93%) rename galaxy/{data_managers/data_manager_mentalist_build_db/tool-data => }/mentalist_databases.loc.sample (100%) create mode 100644 galaxy/mentalist_download.xml create mode 100644 galaxy/tool_data_table_conf.xml.sample create mode 100644 galaxy/tsvs_to_galaxy diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 0000000..a1621ae --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,366 @@ +[[ArgParse]] +deps = ["Logging", "TextWrap"] +git-tree-sha1 = "a8fc2e149cd6db276c76faebe197ccd3a92fb9ff" +uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63" +version = "1.1.0" + +[[Automa]] +deps = ["DataStructures", "Printf", "Random", "Test", "TranscodingStreams"] +git-tree-sha1 = "c81526bf5f6fb4616b4e22a3cd62ac20e255fd3c" +uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" +version = "0.8.0" + +[[Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[BenchmarkTools]] +deps = ["JSON", "Logging", "Printf", "Statistics", "UUIDs"] +git-tree-sha1 = "9e62e66db34540a0c919d72172cc2f642ac71260" +uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +version = "0.5.0" + +[[BinDeps]] +deps = ["Libdl", "Pkg", "SHA", "URIParser", "Unicode"] +git-tree-sha1 = "46cf2c1668ad07aba5a9d331bdeea994a1f13856" +uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee" +version = "1.0.1" + +[[BinaryProvider]] +deps = ["Libdl", "Logging", "SHA"] +git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" +uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" +version = "0.5.10" + +[[BioGenerics]] +deps = ["TranscodingStreams"] +git-tree-sha1 = "57deb413ca9f4c8bc7d4c6e98ebe217ff728c737" +uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea" +version = "0.1.0" + +[[BioSequences]] +deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"] +git-tree-sha1 = "3b04c643d3308b5c4f7f33bb02a578ab1ff13278" +uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" +version = "2.0.4" + +[[BioSymbols]] +deps = ["Automa"] +git-tree-sha1 = "ec77888ac3e78f9d372c2b533bdb52668f9e2b09" +uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9" +version = "4.0.4" + +[[Blosc]] +deps = ["BinaryProvider", "CMakeWrapper", "Libdl"] +git-tree-sha1 = "9981f1795919b8f770dc064fe733ba09c2e7c7a9" +uuid = "a74b3585-a348-5f62-a45c-50e91977d574" +version = "0.6.0" + +[[CMake]] +deps = ["BinDeps"] +git-tree-sha1 = "50a8b41d2c562fccd9ab841085fc7d1e2706da82" +uuid = "631607c0-34d2-5d66-819e-eb0f9aa2061a" +version = "1.2.0" + +[[CMakeWrapper]] +deps = ["BinDeps", "CMake", "Libdl", "Parameters", "Test"] +git-tree-sha1 = "cd82e6082a144e2425bcba6e5fdf5b404401c8e4" +uuid = "d5fb7624-851a-54ee-a528-d3f3bac0b4a0" +version = "0.2.4" + +[[Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + +[[CodecBzip2]] +deps = ["BinaryProvider", "Libdl", "TranscodingStreams"] +git-tree-sha1 = "5db086e510c11b4c87d05067627eadb2dc079995" +uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" +version = "0.6.0" + +[[CodecZlib]] +deps = ["BinaryProvider", "Libdl", "TranscodingStreams"] +git-tree-sha1 = "05916673a2627dd91b4969ff8ba6941bc85a960e" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.6.0" + +[[Combinatorics]] +git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" +uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" +version = "1.0.2" + +[[CommonSubexpressions]] +deps = ["Test"] +git-tree-sha1 = "efdaf19ab11c7889334ca247ff4c9f7c322817b0" +uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +version = "0.2.0" + +[[DataStructures]] +deps = ["InteractiveUtils", "OrderedCollections"] +git-tree-sha1 = "be680f1ad03c0a03796aa3fda5a2180df7f83b46" +uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +version = "0.17.18" + +[[Dates]] +deps = ["Printf"] +uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" + +[[DiffResults]] +deps = ["StaticArrays"] +git-tree-sha1 = "da24935df8e0c6cf28de340b958f6aac88eaa0cc" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.0.2" + +[[DiffRules]] +deps = ["NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "eb0c34204c8410888844ada5359ac8b96292cfd1" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.0.1" + +[[Distributed]] +deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"] +uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" + +[[FileIO]] +deps = ["Pkg"] +git-tree-sha1 = "202335fd24c2776493e198d6c66a6d910400a895" +uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +version = "1.3.0" + +[[ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "869540e4367122fbffaace383a5bdc34d6e5e5ac" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "0.10.10" + +[[GZip]] +deps = ["Libdl"] +git-tree-sha1 = "039be665faf0b8ae36e089cd694233f5dee3f7d6" +uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63" +version = "0.5.1" + +[[Gurobi]] +deps = ["Libdl", "LinearAlgebra", "MathOptInterface", "MathProgBase", "SparseArrays"] +git-tree-sha1 = "f36a2fa62909675681aec582ccfc4a4a629406e4" +uuid = "2e9cd046-0924-5485-92f1-d5272153d98b" +version = "0.8.1" + +[[HDF5]] +deps = ["BinaryProvider", "Blosc", "CMakeWrapper", "Libdl", "Mmap"] +git-tree-sha1 = "d3ea5532668bf9bdd5e8d5f16571e0b520cbbb9f" +uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +version = "0.12.5" + +[[HTTP]] +deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"] +git-tree-sha1 = "ec87d5e2acbe1693789efbbe14f5ea7525758f71" +uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" +version = "0.8.15" + +[[IndexableBitVectors]] +deps = ["Random", "Test"] +git-tree-sha1 = "b7f5e42dc867b8a8654a5f899064632dac05bc82" +uuid = "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d" +version = "1.0.0" + +[[IniFile]] +deps = ["Test"] +git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8" +uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" +version = "0.5.0" + +[[InteractiveUtils]] +deps = ["LinearAlgebra", "Markdown"] +uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" + +[[JLD]] +deps = ["FileIO", "HDF5", "Printf"] +git-tree-sha1 = "f6cf928214ae7c0e7550b2424a57f11875d7e49a" +uuid = "4138dd39-2aa7-5051-a626-17a0bb65d9c8" +version = "0.10.0" + +[[JSON]] +deps = ["Dates", "Mmap", "Parsers", "Unicode"] +git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e" +uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" +version = "0.21.0" + +[[JSONSchema]] +deps = ["HTTP", "JSON", "ZipFile"] +git-tree-sha1 = "832a4d327d9dafdae55a6ecae04f9997c83615cc" +uuid = "7d188eb4-7ad8-530c-ae41-71a32a6d4692" +version = "0.3.0" + +[[JuMP]] +deps = ["Calculus", "DataStructures", "ForwardDiff", "LinearAlgebra", "MathOptInterface", "MutableArithmetics", "NaNMath", "Random", "SparseArrays", "Statistics"] +git-tree-sha1 = "cbab42e2e912109d27046aa88f02a283a9abac7c" +uuid = "4076af6c-e467-56ae-b986-b466b2749572" +version = "0.21.3" + +[[LibGit2]] +uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" + +[[Libdl]] +uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" + +[[LightXML]] +deps = ["BinaryProvider", "Libdl"] +git-tree-sha1 = "be855e3c975b89746b09952407c156b5e4a33a1d" +uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179" +version = "0.8.1" + +[[LinearAlgebra]] +deps = ["Libdl"] +uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + +[[Logging]] +uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" + +[[Markdown]] +deps = ["Base64"] +uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" + +[[MathOptInterface]] +deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "JSONSchema", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "SparseArrays", "Test", "Unicode"] +git-tree-sha1 = "cd2049c055c7d192a235670d50faa375361624ba" +uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" +version = "0.9.14" + +[[MathProgBase]] +deps = ["LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "9abbe463a1e9fc507f12a69e7f29346c2cdc472c" +uuid = "fdba3010-5040-5b88-9595-932c9decdf73" +version = "0.7.8" + +[[MbedTLS]] +deps = ["BinaryProvider", "Dates", "Distributed", "Libdl", "Random", "Sockets", "Test"] +git-tree-sha1 = "2d94286a9c2f52c63a16146bb86fd6cdfbf677c6" +uuid = "739be429-bea8-5141-9913-cc70e7f3736d" +version = "0.6.8" + +[[Mmap]] +uuid = "a63ad114-7e13-5084-954f-fe012c677804" + +[[MutableArithmetics]] +deps = ["LinearAlgebra", "SparseArrays", "Test"] +git-tree-sha1 = "6cf09794783b9de2e662c4e8b60d743021e338d0" +uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" +version = "0.2.10" + +[[NaNMath]] +git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f" +uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" +version = "0.3.3" + +[[OrderedCollections]] +git-tree-sha1 = "12ce190210d278e12644bcadf5b21cbdcf225cd3" +uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +version = "1.2.0" + +[[Parameters]] +deps = ["OrderedCollections", "UnPack"] +git-tree-sha1 = "38b2e970043613c187bd56a995fe2e551821eb4a" +uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" +version = "0.12.1" + +[[Parsers]] +deps = ["Dates", "Test"] +git-tree-sha1 = "eb3e09940c0d7ae01b01d9291ebad7b081c844d3" +uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" +version = "1.0.5" + +[[Pkg]] +deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"] +uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" + +[[Printf]] +deps = ["Unicode"] +uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" + +[[REPL]] +deps = ["InteractiveUtils", "Markdown", "Sockets"] +uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" + +[[Random]] +deps = ["Serialization"] +uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" + +[[SHA]] +uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" + +[[Serialization]] +uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" + +[[Sockets]] +uuid = "6462fe0b-24de-5631-8697-dd941f90decc" + +[[SparseArrays]] +deps = ["LinearAlgebra", "Random"] +uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + +[[SpecialFunctions]] +deps = ["BinDeps", "BinaryProvider", "Libdl"] +git-tree-sha1 = "3bdd374b6fd78faf0119b8c5d538788dbf910c6e" +uuid = "276daf66-3868-5448-9aa4-cd146d93841b" +version = "0.8.0" + +[[StableRNGs]] +deps = ["Random", "Test"] +git-tree-sha1 = "705f8782b1d532c6db75e0a986fb848a629f971a" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "0.1.1" + +[[StaticArrays]] +deps = ["LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "5c06c0aeb81bef54aed4b3f446847905eb6cbda0" +uuid = "90137ffa-7385-5640-81b9-e52037218182" +version = "0.12.3" + +[[Statistics]] +deps = ["LinearAlgebra", "SparseArrays"] +uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + +[[Test]] +deps = ["Distributed", "InteractiveUtils", "Logging", "Random"] +uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[TextWrap]] +git-tree-sha1 = "9250ef9b01b66667380cf3275b3f7488d0e25faf" +uuid = "b718987f-49a8-5099-9789-dcd902bef87d" +version = "1.0.1" + +[[TranscodingStreams]] +deps = ["Random", "Test"] +git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.9.5" + +[[Twiddle]] +git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a" +uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795" +version = "1.1.2" + +[[URIParser]] +deps = ["Unicode"] +git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d" +uuid = "30578b45-9adc-5946-b283-645ec420af67" +version = "0.4.1" + +[[UUIDs]] +deps = ["Random"] +uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" + +[[UnPack]] +git-tree-sha1 = "d4bfa022cd30df012700cf380af2141961bb3bfb" +uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +version = "1.0.1" + +[[Unicode]] +uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[ZipFile]] +deps = ["BinaryProvider", "Libdl", "Printf"] +git-tree-sha1 = "7fbfbc51c186f0ccdbe091f32d3dff8608973f8e" +uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" +version = "0.8.4" diff --git a/README.md b/README.md index 828ad8d..0bddf7a 100644 --- a/README.md +++ b/README.md @@ -32,6 +32,8 @@ The other way is by manually downloading and installing Julia, and the required ### Conda installation +The MentaLiST conda package is maintained [as a bioconda recipe](https://github.com/bioconda/bioconda-recipes/tree/master/recipes/mentalist) + **Note: We've received reports that the current conda builds of MentaLiST are broken. MentaLiST was recently updated to run on Julia 1.1, so these builds are quite out-of-date in respect with the current GitHub version. Until this is resolved, we recommend installing MentaLiST with the manual installation, as described below. ** The easiest way of installing MentaLiST is by creating a new environment with [Conda](https://conda.io/docs/). diff --git a/conda/build.sh b/conda/build.sh deleted file mode 100644 index 3d86bca..0000000 --- a/conda/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -cp -r $SRC_DIR/src/*.jl $PREFIX/bin -cp -r $SRC_DIR/scripts $PREFIX -ln -s $PREFIX/bin/MentaLiST.jl $PREFIX/bin/mentalist -chmod +x $PREFIX/bin/mentalist - -julia -e 'using Pkg; Pkg.add([ "Distributed", "ArgParse", "BioSequences", "JSON", "DataStructures", "JLD", "GZip", "Blosc", "FileIO", "TextWrap", "LightXML", "JuMP", "Gurobi"])' - -rm -f "$PREFIX"/share/julia/site/lib/v*/*.ji -rm -rf "$PREFIX"/share/julia/site/v*/METADATA -rm -f "$PREFIX"/share/julia/site/v*/META_BRANCH diff --git a/conda/meta.yaml b/conda/meta.yaml deleted file mode 100644 index 5ccb017..0000000 --- a/conda/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "1.0.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - git_url: https://github.com/WGS-TB/MentaLiST.git - git_rev: master - -build: - skip: True # [osx] - -requirements: - build: - - julia >=1.0.* - - hdf5 - - mpfr - - libxml2 - run: - - julia >=1.0.* - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/galaxy/data_manager_conf.xml b/galaxy/data_manager_conf.xml new file mode 100644 index 0000000..7e1689e --- /dev/null +++ b/galaxy/data_manager_conf.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + mentalist_databases/${value} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path} + abspath + + + + + + + + + + + + + + + diff --git a/galaxy/data_managers/data_manager_conf.xml b/galaxy/data_managers/data_manager_conf.xml deleted file mode 100644 index 37ae06f..0000000 --- a/galaxy/data_managers/data_manager_conf.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - - - - - - - - mentalist_databases/${value} - - ${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path} - abspath - - - - - - - - - - - - mentalist_databases/${value} - - ${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path} - abspath - - - - - - - - - - - - mentalist_databases/${value} - - ${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path} - abspath - - - - - - - - - - - - mentalist_databases/${value} - - ${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path} - abspath - - - - - diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/.shed.yml b/galaxy/data_managers/data_manager_mentalist_build_db/.shed.yml deleted file mode 100644 index ddd9aa7..0000000 --- a/galaxy/data_managers/data_manager_mentalist_build_db/.shed.yml +++ /dev/null @@ -1,10 +0,0 @@ -categories: -- Data Managers -description: Contains a data manager that defines and populates the mentalist_databases tool data table. -homepage_url: https://github.com/WGS-TB/MentaLiST/ -long_description: | - MentaLiST is based on a k-mer counting algorithm, specifically designed and implemented to handle large typing schemes. -name: data_manager_mentalist_build_db -owner: dfornika -remote_repository_url: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy/data_managers/data_manager_mentalist_build_db -type: unrestricted diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py b/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py deleted file mode 100644 index 8448ac7..0000000 --- a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python -from __future__ import print_function - -import argparse -import os -import subprocess -import sys -import errno -from json import dumps, loads - -DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"] - - -def mentalist_build_db( data_manager_dict, database_name, kmer_size, profile, fasta_files, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - args = [ 'mentalist', 'build_db', '--db', database_name, '-k', str(kmer_size)] - if profile: - args += ['--profile', profile] - print(args) - args += ['--fasta_files'] + fasta_files - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) - data_table_entry = dict( value=database_name, dbkey=database_name, name=database_name, path=database_name ) - for data_table_name in data_table_names: - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - - -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) - return data_manager_dict - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument('params') - parser.add_argument( '-d', '--db', dest='database_name', default=None, help='Database Name' ) - parser.add_argument( '-f', '--fasta_files', dest='fasta_files', nargs='+', default=None, help='FASTA Filenames' ) - parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' ) - parser.add_argument( '-p', '--profile', dest='profile', type=int, default=None, help='Profile' ) - args = parser.parse_args() - - params = loads( open( args.params ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - - try: - os.mkdir( target_directory ) - except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): - pass - else: - raise - - data_manager_dict = {} - - # build the index - mentalist_build_db( data_manager_dict, args.database_name, args.kmer_size, args.profile, args.fasta_files, params, target_directory, DEFAULT_DATA_TABLE_NAMES ) - - # save info to json file - open( args.params, 'wb' ).write( dumps( data_manager_dict ) ) - - -if __name__ == "__main__": - main() diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml b/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml deleted file mode 100644 index 0006432..0000000 --- a/galaxy/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - mentalist - - - - - - - - - - - - - - - 10.1101/172858 - 10.1099/mgen.0.000146 - - diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample b/galaxy/data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample deleted file mode 100644 index f9a9693..0000000 --- a/galaxy/data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample +++ /dev/null @@ -1,8 +0,0 @@ - - - - - value, name, path - -
- \ No newline at end of file diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/.shed.yml b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/.shed.yml deleted file mode 100644 index de34b7c..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/.shed.yml +++ /dev/null @@ -1,10 +0,0 @@ -categories: -- Data Managers -description: Contains a data manager that defines and populates the mentalist_databases tool data table. -homepage_url: https://github.com/WGS-TB/MentaLiST/ -long_description: | - MentaLiST is based on a k-mer counting algorithm, specifically designed and implemented to handle large typing schemes. -name: data_manager_mentalist_download_cgmlst -owner: dfornika -remote_repository_url: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy/data_managers/data_manager_download_cgmlst -type: unrestricted diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py deleted file mode 100644 index e96cbeb..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py +++ /dev/null @@ -1,73 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import os -import string -import subprocess -import sys - -from json import dumps, loads - - -DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"] - - -def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - translation_table = string.maketrans(string.punctuation, ("_" * 32)) - base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst" - today = datetime.date.today().isoformat() - scheme_files_path = base_path + "_scheme_" + today - database_path = base_path + "_k" + str(kmer_size) + "_" + today - database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" - display_name = scheme + " k=" + str(kmer_size) + " (cgMLST) " + today - args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) - data_table_entry = dict( value=database_path, dbkey='cgMLST', name=display_name, path=database_name ) - for data_table_name in data_table_names: - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - - -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) - return data_manager_dict - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument('params') - parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' ) - parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' ) - args = parser.parse_args() - - params = loads( open( args.params ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - - try: - os.mkdir( target_directory ) - except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): - pass - else: - raise - - data_manager_dict = {} - - # build the index - mentalist_download_cgmlst( data_manager_dict, args.kmer_size, args.scheme, params, target_directory, DEFAULT_DATA_TABLE_NAMES ) - - # save info to json file - open( args.params, 'wb' ).write( dumps( data_manager_dict ) ) - - -if __name__ == "__main__": - main() diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml deleted file mode 100644 index 3166ac1..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - - mentalist - - - - - - - - - - - - - - - - - - - - - - - 10.1101/172858 - 10.1099/mgen.0.000146 - - diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool-data/mentalist_databases.loc.sample b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool-data/mentalist_databases.loc.sample deleted file mode 100644 index e69de29..0000000 diff --git a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample b/galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample deleted file mode 100644 index f9a9693..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample +++ /dev/null @@ -1,8 +0,0 @@ - - - - - value, name, path - -
- \ No newline at end of file diff --git a/galaxy/data_managers/data_manager_mentalist_download_enterobase/.shed.yml b/galaxy/data_managers/data_manager_mentalist_download_enterobase/.shed.yml deleted file mode 100644 index 93a0d6a..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_enterobase/.shed.yml +++ /dev/null @@ -1,11 +0,0 @@ -categories: -- Data Managers -- Metagenomics -description: Contains a data manager that defines and populates the mentalist_databases tool data table. -homepage_url: https://github.com/WGS-TB/MentaLiST/ -long_description: | - MentaLiST is based on a k-mer counting algorithm, specifically designed and implemented to handle large typing schemes. -name: data_manager_mentalist_download_enterobase -owner: dfornika -remote_repository_url: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy/data_managers/data_manager_mentalist_download_enterobase -type: unrestricted diff --git a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py b/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py deleted file mode 100644 index 59986ec..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py +++ /dev/null @@ -1,79 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import os -import string -import subprocess -import sys - -from json import dumps, loads - - -DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"] - - -def mentalist_download_enterobase( data_manager_dict, kmer_size, scheme, type, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - char_to_full_organism_name = { - 'E': 'Escherichia/Shigella', - 'S': 'Salmonella', - 'Y': 'Yersinia' - } - translation_table = string.maketrans(string.punctuation, ("_" * 32)) - base_path = char_to_full_organism_name[scheme].lower().replace(" ", "_").translate(translation_table) + "_enterobase" - today = datetime.date.today().isoformat() - scheme_files_path = base_path + "_scheme_" + today - database_path = base_path + "_k" + str(kmer_size) + "_" + today - database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" - display_name = char_to_full_organism_name[scheme] + " k=" + str(kmer_size) + " (Enterobase) " + today - args = [ 'mentalist', 'download_enterobase', '-s', scheme, '-t', type, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) - data_table_entry = dict( value=database_path, dbkey='Enterobase', name=display_name, path=database_name ) - for data_table_name in data_table_names: - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - - -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) - return data_manager_dict - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument('params') - parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help="Scheme: ('E'=Escherichia/Shigella, 'S'=Salmonella, 'Y'=Yersinia)") - parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' ) - parser.add_argument( '-t', '--type', dest='type', default=None, help="Type: ('cg'=cgMLST, 'wg'=wgMLST')") - args = parser.parse_args() - - params = loads( open( args.params ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - - try: - os.mkdir( target_directory ) - except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): - pass - else: - raise - - data_manager_dict = {} - - # build the index - mentalist_download_enterobase( data_manager_dict, args.kmer_size, args.scheme, args.type, params, target_directory, DEFAULT_DATA_TABLE_NAMES ) - - # save info to json file - open( args.params, 'wb' ).write( dumps( data_manager_dict ) ) - - -if __name__ == "__main__": - main() diff --git a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml b/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml deleted file mode 100644 index 5fcee83..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml +++ /dev/null @@ -1,35 +0,0 @@ - - - - mentalist - - - - - - - - - - - - - - - - - - - - - 10.1101/172858 - - diff --git a/galaxy/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample b/galaxy/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample deleted file mode 100644 index f9a9693..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample +++ /dev/null @@ -1,8 +0,0 @@ - - - - - value, name, path - -
- \ No newline at end of file diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/.shed.yml b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/.shed.yml deleted file mode 100644 index 25cf705..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/.shed.yml +++ /dev/null @@ -1,11 +0,0 @@ -categories: -- Data Managers -- Metagenomics -description: Contains a data manager that defines and populates the mentalist_databases tool data table. -homepage_url: https://github.com/WGS-TB/MentaLiST/ -long_description: | - MentaLiST is based on a k-mer counting algorithm, specifically designed and implemented to handle large typing schemes. -name: data_manager_mentalist_download_pubmlst -owner: dfornika -remote_repository_url: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy/data_managers/data_manager_mentalist_download_pubmlst -type: unrestricted diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py deleted file mode 100644 index d51dc47..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import os -import string -import subprocess -import sys - -from json import dumps, loads - - -DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"] - - -def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - scheme = scheme.replace('__pd__','#') - translation_table = string.maketrans(string.punctuation, ("_" * 32)) - base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst" - today = datetime.date.today().isoformat() - scheme_files_path = base_path + "_scheme_" + today - database_path = base_path + "_k" + str(kmer_size) + "_" + today - database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" - display_name = scheme + " k=" + str(kmer_size) + " (PubMLST) " + today - args = [ 'mentalist', 'download_pubmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) - return_code = proc.wait() - if return_code: - print("Error building database.", file=sys.stderr) - sys.exit( return_code ) - data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=database_name ) - for data_table_name in data_table_names: - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - - -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) - return data_manager_dict - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument('params') - parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' ) - parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' ) - args = parser.parse_args() - - params = loads( open( args.params ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - - try: - os.mkdir( target_directory ) - except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): - pass - else: - raise - - data_manager_dict = {} - - # build the index - mentalist_download_pubmlst( data_manager_dict, args.kmer_size, args.scheme, params, target_directory, DEFAULT_DATA_TABLE_NAMES ) - - # save info to json file - open( args.params, 'wb' ).write( dumps( data_manager_dict ) ) - - -if __name__ == "__main__": - main() diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml deleted file mode 100644 index 4562897..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml +++ /dev/null @@ -1,161 +0,0 @@ - - - - mentalist - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1101/172858 - 10.1099/mgen.0.000146 - - diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool-data/mentalist_databases.loc.sample b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool-data/mentalist_databases.loc.sample deleted file mode 100644 index e69de29..0000000 diff --git a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample b/galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample deleted file mode 100644 index f9a9693..0000000 --- a/galaxy/data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample +++ /dev/null @@ -1,8 +0,0 @@ - - - - - value, name, path - -
- \ No newline at end of file diff --git a/galaxy/enterobase.tsv b/galaxy/enterobase.tsv new file mode 100644 index 0000000..3a90f00 --- /dev/null +++ b/galaxy/enterobase.tsv @@ -0,0 +1,4 @@ +S Salmonella +Y Yersinia +E Escherichia/Shigella +C clostridium \ No newline at end of file diff --git a/galaxy/tools/mentalist_call/mentalist_call.xml b/galaxy/mentalist_call.xml similarity index 93% rename from galaxy/tools/mentalist_call/mentalist_call.xml rename to galaxy/mentalist_call.xml index e3941f1..5cc642c 100644 --- a/galaxy/tools/mentalist_call/mentalist_call.xml +++ b/galaxy/mentalist_call.xml @@ -1,6 +1,6 @@ - + - mentalist + mentalist operation_3840 @@ -36,7 +36,7 @@ - + - diff --git a/galaxy/data_managers/data_manager_mentalist_build_db/tool-data/mentalist_databases.loc.sample b/galaxy/mentalist_databases.loc.sample similarity index 100% rename from galaxy/data_managers/data_manager_mentalist_build_db/tool-data/mentalist_databases.loc.sample rename to galaxy/mentalist_databases.loc.sample diff --git a/galaxy/mentalist_download.xml b/galaxy/mentalist_download.xml new file mode 100644 index 0000000..140c0a1 --- /dev/null +++ b/galaxy/mentalist_download.xml @@ -0,0 +1,100 @@ + + + + mentalist + jq + + '$output' + #else + mentalist '$mode_selection.mode' -k '$mode_selection.kmer_size' + #if $mode_selection.mode == 'build_db' + #set unique_id = "${mode_select.scheme}_${ re.sub('\W', '_', str(mode_select.database_name)) }_${mode_selection.kmer_size}" + #set name = "${mode_selection.database_name} k=${mode_selection.kmer_size} (${mode_selection.scheme})" + --db '${unique_id}.jld' + #if $mode_selection.profile + --profile '$mode_selection.profile' + #end if + --fasta_files + #for fasta in $mode_selection.input_fastas + '$fasta' + #end for + #else + #set scheme_name = next(record for record in $__app__.tool_data_tables['mlst_db_sources'].get_fields() if str( record[1] ) == str( $mode_selection.database_name ) and str( record[2] ) == str( $mode_selection.scheme ))[-1] + #set unique_id = "${mode_select.database_name}_${mode_select.scheme}_${mode_selection.kmer_size}" + #set name = "${scheme_name} k=${mode_selection.kmer_size} (${mode_selection.database_name}" + (" $mode_selection.type" if $mode_selection.type else "") + ")" + #if $mode_selection.type + #set unique_id = $unique_id + "_${mode_selection.type}" + -t '$mode_selection.type' + #end if + --db '${unique_id}.jld' + -o '${unique_id}' + #end if + && echo '{"data_tables":{"mentalist_databases":[{"value":"${unique_id}","name":"$name","path":"${unique_id}.jld"}]}}' > '$output' + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1101/172858 + 10.1099/mgen.0.000146 + + diff --git a/galaxy/tool_data_table_conf.xml.sample b/galaxy/tool_data_table_conf.xml.sample new file mode 100644 index 0000000..0a5a5a7 --- /dev/null +++ b/galaxy/tool_data_table_conf.xml.sample @@ -0,0 +1,12 @@ + + + + + value, name, path + +
+ + source_id, source, id, name + +
+ \ No newline at end of file diff --git a/galaxy/tsvs_to_galaxy b/galaxy/tsvs_to_galaxy new file mode 100644 index 0000000..7c7f187 --- /dev/null +++ b/galaxy/tsvs_to_galaxy @@ -0,0 +1,10 @@ +def parseTSV: . | split("\n") | map(select(startswith("#") | not)) | map(split("\t")) | .[]; +{ + "data_tables": { + "mlst_db_sources": [ + ($pb | parseTSV | {"source_id": "pubMLST_" + .[0], source": "pubMLST", "id": .[0], "name": .[1]}) + + ($cg | parseTSV | {"source_id": "cgMLST_" + .[0], "source": "cgMLST", "id": .[0], "name": .[1]}) + + ($eb | parseTSV | {"source_id": "Enterobase_" + .[0], "source": "Enterobase", "id": .[0], "name": .[1]}) + ] + } +} From f467939507be9d3596416e7ed60ba2422e86adf1 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Mon, 22 Jun 2020 10:08:49 -0700 Subject: [PATCH 3/5] Set tool to Galaxy 18.09 profile to avoid legacy mode --- galaxy/mentalist_call.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/mentalist_call.xml b/galaxy/mentalist_call.xml index 5cc642c..3eda241 100644 --- a/galaxy/mentalist_call.xml +++ b/galaxy/mentalist_call.xml @@ -1,4 +1,4 @@ - + mentalist From 55d8b2516042679c77b4fb5d32aa54ffa367d13b Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Mon, 22 Jun 2020 10:09:25 -0700 Subject: [PATCH 4/5] Bump mentalist version for call tool --- galaxy/mentalist_call.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/galaxy/mentalist_call.xml b/galaxy/mentalist_call.xml index 3eda241..cc3dac8 100644 --- a/galaxy/mentalist_call.xml +++ b/galaxy/mentalist_call.xml @@ -1,6 +1,6 @@ - + - mentalist + mentalist operation_3840 From bd3f1d86e47792a34bb56db4913078c74eba16b1 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Mon, 22 Jun 2020 14:06:38 -0700 Subject: [PATCH 5/5] Decrement mentalist version to latest release --- galaxy/data_manager_conf.xml | 2 +- galaxy/mentalist_call.xml | 2 +- galaxy/mentalist_download.xml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/galaxy/data_manager_conf.xml b/galaxy/data_manager_conf.xml index 7e1689e..f9f9b6a 100644 --- a/galaxy/data_manager_conf.xml +++ b/galaxy/data_manager_conf.xml @@ -1,6 +1,6 @@ - + diff --git a/galaxy/mentalist_call.xml b/galaxy/mentalist_call.xml index cc3dac8..f48834c 100644 --- a/galaxy/mentalist_call.xml +++ b/galaxy/mentalist_call.xml @@ -1,4 +1,4 @@ - + mentalist diff --git a/galaxy/mentalist_download.xml b/galaxy/mentalist_download.xml index 140c0a1..5b406dc 100644 --- a/galaxy/mentalist_download.xml +++ b/galaxy/mentalist_download.xml @@ -1,7 +1,7 @@ - + - mentalist + mentalist jq