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| diff -r 4ac32c671a40 -r acbcdd5b4c60 README.rst --- a/README.rst Wed Jan 15 13:34:02 2020 -0500 +++ b/README.rst Wed Jan 15 14:43:05 2020 -0500 |
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| @@ -1,33 +1,37 @@ -Configuration of Galaxy to run GLASSgo in Docker -================================================ +Configuration of Galaxy to run GLASSgo via 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 +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">$defaults,/Volumes/TC1/nt:/Volumes/TC1/nt/</param>` + `<param id="docker_volumes">$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. + 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. +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. + + - manually + download the accession lists from Zenodo (https://zenodo.org/record/1320180) and add the corresponding paths to the file + glassgo_accession_list.txt Afterwards, copy the file into the folder tool-data of Galaxy (e.g., /galaxy/tool-data/) or + - using the script + use the config_lookup script that downloads the lookup tables and creates glassgo_accession_list.txt in tool-data of the Galaxy instance. - - 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. +Restart Galaxy. config_lookup ------------- +We provide the source file config_lookup.py as well as a one-file bundled executable config_lookup ` -usage: config_lookup [-h] --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS] +usage: config_lookup [-h] --galaxy GALAXY [--acclinks ACCLINKS --acclists ACCLISTS] incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches |