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author computationaltranscriptomics
date Wed, 15 Jan 2020 14:43:05 -0500
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1 Configuration of Galaxy to run GLASSgo in Docker 1 Configuration of Galaxy to run GLASSgo via Docker
2 ================================================ 2 =================================================
3 3
4 Prerequisites 4 Prerequisites
5 ------------- 5 -------------
6 6
7 1) configure Galaxy to run tools in Docker as described at \ 7 1) configure Galaxy to run tools in Docker as described at https://galaxyproject.org/admin/tools/docker/.
8 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). 8 In addition, GLASSgo requires the current BLAST nucleotide database. For that, the `tool-data/blastdb.loc`
9 For that, we add Docker volumes to the (id=`docker_local`) Docker destination 9 has to be configured accordingly as the GLASSgo wrapper reads this information as options when laying out
10 the user interface. We use Docker volumes to do so (Docker CLI option -v). For that, we add Docker volumes
11 to the (id=`docker_local`) Docker destination
10 12
11 `<param id="docker_volumes">$defaults,/Volumes/TC1/nt:/Volumes/TC1/nt/</param>` 13 `<param id="docker_volumes">$defaults,/Volumes/TC1/nt:/Volumes/TC1/nt/</param>`
12 14
13 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. 15 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.
14 16
15 2) Install GLASSgo from the Galaxy Toolshed 17 2) Install GLASSgo from the Galaxy Toolshed (https://toolshed.g2.bx.psu.edu/view/computationaltranscriptomics/glassgo).
16 (https://toolshed.g2.bx.psu.edu/view/computationaltranscriptomics/glassgo). 18 Afterwards, the Galaxy instance needs to be configured such that it is aware of the accession lists. This can be done either
17 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. 19 manually or using a custom script.
20
21 - manually
22 download the accession lists from Zenodo (https://zenodo.org/record/1320180) and add the corresponding paths to the file
23 glassgo_accession_list.txt Afterwards, copy the file into the folder tool-data of Galaxy (e.g., /galaxy/tool-data/) or
24 - using the script
25 use the config_lookup script that downloads the lookup tables and creates glassgo_accession_list.txt in tool-data of the Galaxy instance.
18 26
19 - 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 27 Restart Galaxy.
20
21 - use `config_lookup` (./config_lookup/dist/) to download the look tables using `accession_lists_links.txt`(./accession_lists_links.txt)
22 (option --acclinks) and creates `glassgo_accession_list.txt` in `tool-data` of Galaxy.
23
24 Note: Any changes of files within `tool-data` requires a (re)start of Galaxy.
25 28
26 29
27 config_lookup 30 config_lookup
28 ------------- 31 -------------
32 We provide the source file config_lookup.py as well as a one-file bundled executable config_lookup
29 ` 33 `
30 usage: config_lookup [-h] --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS] 34 usage: config_lookup [-h] --galaxy GALAXY [--acclinks ACCLINKS --acclists ACCLISTS]
31 35
32 incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches 36 incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches
33 37
34 optional arguments: 38 optional arguments:
35 -h, --help show this help message and exit 39 -h, --help show this help message and exit