diff --git a/data_managers/data_manager_build_coreprofiler/data_manager/data_manager_build_coreprofiler_download.xml b/data_managers/data_manager_build_coreprofiler/data_manager/data_manager_build_coreprofiler_download.xml index 20e1729108c..cab048795b8 100644 --- a/data_managers/data_manager_build_coreprofiler/data_manager/data_manager_build_coreprofiler_download.xml +++ b/data_managers/data_manager_build_coreprofiler/data_manager/data_manager_build_coreprofiler_download.xml @@ -1,7 +1,7 @@ - 1.1.7 + 1.1.8 0 22.05 @@ -27,10 +27,14 @@ blast - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -164,8 +234,11 @@ cp '$dmjson' '$out_file' - - + + + + + @@ -179,8 +252,11 @@ cp '$dmjson' '$out_file' - - + + + + + @@ -194,8 +270,10 @@ cp '$dmjson' '$out_file' - - + + + + @@ -207,89 +285,119 @@ cp '$dmjson' '$out_file' + + + + + + + + + + + + + + + + + CoreProfiler documentation. +CoreProfiler supports several reference platforms: + +- **pubMLST** +- **BIGSdb** +- **EnteroBase** +- **cgMLST.org** + +The list of available schemes is maintained in the `CoreProfiler documentation `_. Please refer to this page for details on how to use the tool and which schema options are available. -Use Galaxy's data manager framework to download and install new CoreProfiler schemes : +You simply need to choose: +1. A reference platform +2. A scheme available on that platform +3. Whether authentication is required (pubMLST / BIGSdb only) -If you want to use a scheme from enterobase, you do not need to provide any token or secret. +Galaxy will download the database, build the scheme, and register it automatically. -However, if you want to use a scheme from **pubMLST** or **BigsDB**, you will need to follow a procedure before launching the data manager. +--- -BIGSdb and PubMLST platforms require OAuth1 authentication to access and download the most up-to-date schemes. -While authentication is not strictly mandatory, skipping it may result in downloading outdated schemes. +Authentication requirements +--------------------------- -This authentication involves two types of tokens: +Authentication is **not needed** for: - * Consumer tokens : permanent tokens used to initiate the authentication flow. +- **EnteroBase** +- **cgMLST.org** - * Access tokens : tokens required to download a scheme. -Procedure for pubMLST schemes (example with borrelia_3-cgMLST-639-pubmlst) : +Authentication **is recommended** for: + +- **pubMLST** +- **BIGSdb** -1. Create an account on the pubMLST website. -2. Generate a consumer token and secret from your account settings (My account > API keys > Enter key name > Submit). -3. On your account page, go to Database registrations, check all databases and register. -4. Download coreprofiler locally and run the following command to obtain your access token and secret -Replace the placeholders with your scheme of interest (example : borrelia_3) your actual consumer token and secret : +Why? +```` -""" -coreprofiler db get_request_tokens --scheme --consumer_key --consumer_secret -""" +BIGSdb and pubMLST platforms require **OAuth1** authentication and restrict access to the most up-to-date data. +While authentication is not strictly mandatory, skipping it may result in downloading **outdated** schemes. -This command will provide you with a URL to visit in order to authorize client software to access your account. -After authorizing, it will give you a verification code that you need to enter in the command line prompt. +This authentication involves two types of tokens: + + * Consumer tokens : permanent tokens used to initiate the authentication flow. + + * Access tokens : tokens required to download a scheme. + +--- -It will then return your access token and secret. +Procedure to obtain pubMLST and BIGSdb schemes +---------------------------------------------- -5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : +Example +``````` +- **pubMLST**: borrelia_3-cgMLST-639-pubmlst +- **BIGSdb**: bordetella_1-cgMLST_genus-1415-BIGSdb -""" -export COREPROFILER_CONSUMER_TOKEN="" -export COREPROFILER_CONSUMER_SECRET="" -export COREPROFILER_ACCESS_TOKEN="" -export COREPROFILER_ACCESS_SECRET="" -""" +1. Create an account on the `pubMLST `_ or `BigsDB `_ website. +2. Generate a **consumer token** and **consumer secret** + * **pubMLST**: From your account settings (My account > API keys > Enter key name > Submit). + * **BIGSdb**: By sending a mail to bigsdb@pasteur.fr (object "API client key"). +3. On your account page, go to **Database registrations**, check all databases and register. +4. Download and install `coreprofiler `_ locally and run the following command to **obtain your access token and secret** -6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"). +Replace the placeholders with your scheme of interest (example : *borrelia_3* or *bordetella_1*) your actual consumer token and secret : -Procedure for BigsDB (example with bordetella_1-cgMLST_genus-1415-BIGSdb): +:: -1. Create an account on the BigsDB website. -2. Ask for a consumer token and secret by sending a mail to bigsdb@pasteur.fr (object "API client key"). -3. On your account page, go to Database registrations, check all databases and register. -4. Download coreprofiler locally and run the following command to obtain your access token and secret + coreprofiler db get_request_tokens --scheme --consumer_key --consumer_secret -Replace the placeholders with your scheme of interest (example : bordetella_1) your actual consumer token and secret : -""" -coreprofiler db get_request_tokens --scheme --consumer_key --consumer_secret -""" +This command will provide you with a URL to visit in order to **authorize client software** to access your account. +After authorizing, it will give you a **verification code** that you need to enter in the command line prompt. +It will then return **your access token and secret**. -This command will provide you with a URL to visit in order to authorize client software to access your account. +5. Provide the **consumer token**, **consumer secret**, **access token**, and **access secret** in the data manager tool by setting this bash variables in a txt file : -After authorizing, it will give you a verification code that you need to enter in the command line prompt. +:: -It will then return your access token and secret. + export COREPROFILER_CONSUMER_TOKEN="" + export COREPROFILER_CONSUMER_SECRET="" + export COREPROFILER_ACCESS_TOKEN="" + export COREPROFILER_ACCESS_SECRET="" -5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : -""" -export COREPROFILER_CONSUMER_TOKEN="" -export COREPROFILER_CONSUMER_SECRET="" -export COREPROFILER_ACCESS_TOKEN="" -export COREPROFILER_ACCESS_SECRET="" -""" +6. Set the **path** to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"). -6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"). - ]]> +]]> 10.3390/microorganisms10020292 diff --git a/data_managers/data_manager_build_coreprofiler/test-data/coreprofiler_scheme.loc.test b/data_managers/data_manager_build_coreprofiler/test-data/coreprofiler_scheme.loc.test index 4940dee5e53..dbc203d36ea 100644 --- a/data_managers/data_manager_build_coreprofiler/test-data/coreprofiler_scheme.loc.test +++ b/data_managers/data_manager_build_coreprofiler/test-data/coreprofiler_scheme.loc.test @@ -16,3 +16,19 @@ coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token coreprofiler_downloaded_17112025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 coreprofiler_downloaded_17112025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_01122025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmp_1vwak4i/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_01122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmp_1vwak4i/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_01122025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmp_1vwak4i/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_01122025-mgallisepticum1387-Mycoplasma_gallisepticum-425-cgmlstorg-no_token mgallisepticum1387: Mycoplasma_gallisepticum [425 loci] (cgmlstorg-no_token) /tmp/tmp_1vwak4i/galaxy-dev/tool-data/coreprofiler/coreprofiler_mgallisepticum1387_no_token coreprofiler_mgallisepticum1387_no_token/db_mgallisepticum1387/mgallisepticum1387.fasta coreprofiler_mgallisepticum1387_no_token/scheme_mgallisepticum1387 +coreprofiler_downloaded_01122025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmpdb0g14st/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_01122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmpdb0g14st/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_01122025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmpdb0g14st/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_01122025-mgallisepticum1387-Mycoplasma_gallisepticum-425-cgmlstorg-no_token mgallisepticum1387: Mycoplasma_gallisepticum [425 loci] (cgmlstorg-no_token) /tmp/tmpdb0g14st/galaxy-dev/tool-data/coreprofiler/coreprofiler_mgallisepticum1387_no_token coreprofiler_mgallisepticum1387_no_token/db_mgallisepticum1387/mgallisepticum1387.fasta coreprofiler_mgallisepticum1387_no_token/scheme_mgallisepticum1387 +coreprofiler_downloaded_01122025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmp_fet2bll/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_01122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmp_fet2bll/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_01122025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmp_fet2bll/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_01122025-mgallisepticum1387-Mycoplasma_gallisepticum-425-cgmlstorg-no_token mgallisepticum1387: Mycoplasma_gallisepticum [425 loci] (cgmlstorg-no_token) /tmp/tmp_fet2bll/galaxy-dev/tool-data/coreprofiler/coreprofiler_mgallisepticum1387_no_token coreprofiler_mgallisepticum1387_no_token/db_mgallisepticum1387/mgallisepticum1387.fasta coreprofiler_mgallisepticum1387_no_token/scheme_mgallisepticum1387 +coreprofiler_downloaded_02122025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmphpm09w2g/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_02122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmphpm09w2g/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_02122025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmphpm09w2g/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_02122025-mgallisepticum1387-Mycoplasma_gallisepticum-425-cgmlstorg-no_token mgallisepticum1387: Mycoplasma_gallisepticum [425 loci] (cgmlstorg-no_token) /tmp/tmphpm09w2g/galaxy-dev/tool-data/coreprofiler/coreprofiler_mgallisepticum1387_no_token coreprofiler_mgallisepticum1387_no_token/db_mgallisepticum1387/mgallisepticum1387.fasta coreprofiler_mgallisepticum1387_no_token/scheme_mgallisepticum1387 diff --git a/tools/coreprofiler/macro.xml b/tools/coreprofiler/macro.xml index 624f2fa714f..cfe193462ff 100644 --- a/tools/coreprofiler/macro.xml +++ b/tools/coreprofiler/macro.xml @@ -1,6 +1,6 @@ - 1.1.7 + 1.1.8 0 22.05