Skip to content

Commit 6234105

Browse files
Update README.md Ansible
1 parent a019149 commit 6234105

File tree

1 file changed

+25
-29
lines changed

1 file changed

+25
-29
lines changed

README.md

Lines changed: 25 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -1,32 +1,28 @@
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+
&ensp;&ensp;`file: otutab_trim.xml`
25+
&ensp;&ensp;`version: master`
426

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-
```
3127
## Source
3228
https://www.drive5.com/usearch/manual/cmd_otutab_trim.html

0 commit comments

Comments
 (0)