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1 | | -# galaxy-tool-otutab_trim |
2 | | -## Getting Started |
3 | | -### Prerequisites |
| 1 | +# galaxy-tool-otutab_trim |
| 2 | +Trim records from otu-table that don't meet set threshold values. |
| 3 | + |
| 4 | +### Prerequisites |
| 5 | +**USEARCH** should be installed. This will be the case if **make OTU table** was priorly installed. |
| 6 | +If not, follow the [instructions there](https://github.com/naturalis/galaxy-tool-make-otu-table#prerequisites). |
| 7 | + |
| 8 | +## Installation |
| 9 | +### Manual |
| 10 | +Clone this repo in your Galaxy ***Tools*** directory: |
| 11 | +`git clone https://github.com/naturalis/galaxy-tool-otutab_trim` |
| 12 | + |
| 13 | +Make sure the scripts are executable: |
| 14 | +`chmod 755 galaxy-tool-otutab_trim/otutab_trim.sh` |
| 15 | + |
| 16 | +Append the file ***tool_conf.xml***: |
| 17 | +`<tool file="/path/to/Tools/galaxy-tool-otutab_trim/otutab_trim.xml" />` |
| 18 | + |
| 19 | +### Ansible |
| 20 | +Depending on your setup the [ansible.builtin.git](https://docs.ansible.com/ansible/latest/collections/ansible/builtin/git_module.html) module could be used. |
| 21 | +[Install the tool](https://docs.ansible.com/ansible/latest/collections/ansible/builtin/git_module.html#examples) by including the following in your dedicated ***.yml** file: |
| 22 | + |
| 23 | +` - repo: https://github.com/naturalis/galaxy-tool-otutab_trim` |
| 24 | +  `file: otutab_trim.xml` |
| 25 | +  `version: master` |
4 | 26 |
|
5 | | -**USEARCH**<br /> |
6 | | -**Note:** proceed with **Installing** if [make OTU table](https://github.com/naturalis/galaxy-tool-make-otu-table) was priorly installed. |
7 | | -(user: **galaxy**) |
8 | | -``` |
9 | | -mkdir /home/galaxy/Tools/usearch |
10 | | -cd /home/galaxy/Tools/usearch |
11 | | -wget [your usearch licence] |
12 | | -mv [your usearch licence] usearch11 |
13 | | -chmod 777 /home/galaxy/Tools/usearch/usearch11 |
14 | | -``` |
15 | | -(user: **ubuntu**) |
16 | | -``` |
17 | | -sudo ln -s /home/galaxy/Tools/usearch/usearch11 /usr/local/bin/usearch11 |
18 | | -``` |
19 | | -### Installing |
20 | | -Installing the tool for use in Galaxy |
21 | | -(user: **galaxy**) |
22 | | -``` |
23 | | -cd /home/galaxy/Tools |
24 | | -git clone https://github.com/naturalis/galaxy-tool-otutab_trim |
25 | | -chmod 777 galaxy-tool-otutab_trim/* |
26 | | -``` |
27 | | -Add the following line to /home/galaxy/galaxy/config/tool_conf.xml |
28 | | -``` |
29 | | -<tool file="/home/galaxy/Tools/galaxy-tool-otutab_trim/otutab_trim.xml" /> |
30 | | -``` |
31 | 27 | ## Source |
32 | 28 | https://www.drive5.com/usearch/manual/cmd_otutab_trim.html |
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