Mercurial > repos > tduigou > rp2paths
annotate README.md @ 2:2452952f7bc2 draft
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
author | tduigou |
---|---|
date | Mon, 03 Apr 2023 08:15:46 +0000 |
parents | |
children |
rev | line source |
---|---|
2
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
1 # rp2paths -- Enumerate and seperate the different pathways generated by RetroPath2.0 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
2 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
3 The open-source software package rp2paths is available here : https://github.com/brsynth/rp2paths |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
4 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
5 ## How to run rp2paths wrapper tests |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
6 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
7 In order to execute tests on rp2paths wrapper, you need to: |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
8 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
9 - Connect to your galaxy instance in interactive mode: |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
10 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
11 ```bash |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
12 docker exec -it -u root galaxy_galaxy_1 bash |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
13 ``` |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
14 - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
15 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
16 - Install Planemo: |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
17 You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
18 Note that they recommand to install Planemo by setting up a virtual environment: |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
19 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
20 ```bash |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
21 python3 -m venv planemo |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
22 . planemo/bin/activate |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
23 pip install -U planemo |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
24 ``` |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
25 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
26 - run the tests: |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
27 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
28 ```bash |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
29 planemo test --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/rp2paths/wrap.xml |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
30 ``` |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
31 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
32 IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
33 |
2452952f7bc2
planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
tduigou
parents:
diff
changeset
|
34 Planemo will output an html test summary `tool_test_output.html`. |