Skip to content

Correct the stale parts of the README #12

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
bmesuere wants to merge 1 commit into
base: phase1/ci-and-test-fix
Choose a base branch
from
Open

Correct the stale parts of the README #12

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 16 additions & 6 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,12 @@ Statistics at [Ghent University].

1. Install [Rust], according to [their installation instructions][rust-install],
or use your favourite package manager (e.g. `apt install rustc`). The
pipeline is developed for the latest stable release, but should work on 1.35
and higher.
pipeline is developed for the latest stable release and needs at least Rust
1.88.

2. Clone this repository and go to the repository root.
2. Clone this repository and go to the repository root. The preconfigured
pipelines and the setup script live here; they are not part of the published
crate.

```sh
git clone https://github.com/unipept/umgap.git
Expand All @@ -29,6 +31,13 @@ Statistics at [Ghent University].
cargo install --path .
```

If you only need the `umgap` command itself and not the pipeline scripts,
you can skip the clone and install it from [crates.io][crate] instead:

```sh
cargo install umgap
```

For a multiuser installation, instead of `cargo install`, use `install` to
place the umgap program and the wrapper script were all users can reach it:

Expand Down Expand Up @@ -73,10 +82,10 @@ Statistics at [Ghent University].
./scripts/umgap-analyse.sh -1 testdata/A1.fq -2 testdata/A2.fq -o - | tee output.fa
```

7. (optional) NOT YET INTEGRATED - Visualize some test data! Running
7. (optional) Visualize some test data! Running

```sh
./scripts/umgap-visualize.sh output.fa output.html
./scripts/umgap-visualize.sh -w output.fa > output.html
```

will give you an HTML-file, which will show you a visualization of the test
Expand Down Expand Up @@ -133,7 +142,8 @@ for more info.
[Unipept]: https://unipept.ugent.be/
[Ghent University]: https://www.ugent.be/
[Rust]: https://www.rust-lang.org/
[metagenomics casestudy]: https://unipept.ugent.be/clidocs/casestudies/metagenomics
[metagenomics casestudy]: https://unipept.ugent.be/umgap/casestudies
[crate]: https://crates.io/crates/umgap
[rust-install]: https://www.rust-lang.org/tools/install
[FragGeneScanPlusPlus]: https://github.com/unipept/FragGeneScanPlusPlus
[EditorConfig]: https://editorconfig.org/
Expand Down
Loading