Mercurial > repos > galaxyp > openms_openswathworkflow

comparison readme.md @ 3:372279190f47 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 19:07:41 -0400
parents a46df1a24002
children 9efa5698412b
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2:a46df1a24002 3:372279190f47
12 12
13 13
14 Generating OpenMS wrappers 14 Generating OpenMS wrappers
15 ========================== 15 ==========================
16 16
17 * install OpenMS (you can do this automatically through the Tool Shed) 17 * install OpenMS (you can do this automatically through Conda)
18 * create a folder called CTD 18 * create a folder called CTD
19 * inside of your new installed openms/bin folder, execute the following command: 19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
20 20
21 ```bash 21 ```bash
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; 22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
23 ``` 23 ```
24 24
25 * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). 25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
26
27 ```bash
28 ls >> tools.txt
29 ```
30
31 * search for the `bin` folder of your conda environment containing OpenMS and do:
32
33 ```bash
34 while read p; do
35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
36 done <tools.txt
37 ```
38
39 * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
26 40
27 * clone or install CTDopts 41 * clone or install CTDopts
28 42
29 ```bash 43 ```bash
30 git clone https://github.com/genericworkflownodes/CTDopts 44 git clone https://github.com/genericworkflownodes/CTDopts
40 54
41 ```bash 55 ```bash
42 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git 56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
43 ``` 57 ```
44 58
45 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. 59 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
46 60
47 ```bash 61 ```bash
48 python generator.py \ 62 python generator.py \
49 -i /PATH/TO/YOUR/CTD/*.ctd \ 63 -i /PATH/TO/YOUR/CTD/*.ctd \
50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ 64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \