From 9acec18d0b213a8f1bc25e3e7ba2364ec62db46d Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 24 Apr 2024 13:15:45 +0200 Subject: [PATCH 1/6] Update README.md In response to https://github.com/jotech/gapseq/issues/60 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 769c5e12..8a1571d6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # gapseq _Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks_ [![Documentation Status](https://readthedocs.org/projects/gapseq/badge/?version=latest)](https://gapseq.readthedocs.io/en/latest/?badge=latest) -[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) +[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) [![conda build](https://img.shields.io/conda/v/bioconda/gapseq)]([#installation](https://bioconda.github.io/recipes/gapseq/README.html)) _gapseq_ is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. From 7570307257f8451a8b57d475a0189ab4c6dbce2b Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 24 Apr 2024 13:17:42 +0200 Subject: [PATCH 2/6] Add badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8a1571d6..aa6c429f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # gapseq _Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks_ [![Documentation Status](https://readthedocs.org/projects/gapseq/badge/?version=latest)](https://gapseq.readthedocs.io/en/latest/?badge=latest) -[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) [![conda build](https://img.shields.io/conda/v/bioconda/gapseq)]([#installation](https://bioconda.github.io/recipes/gapseq/README.html)) +[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) [![conda build](https://img.shields.io/conda/v/bioconda/gapseq)](https://bioconda.github.io/recipes/gapseq/README.html) _gapseq_ is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. From d920f5a7a122da97f1f7b36276ac63cda00a5d84 Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 24 Apr 2024 13:22:16 +0200 Subject: [PATCH 3/6] Add brief installation instructions --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index aa6c429f..06848c11 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,12 @@ git clone https://github.com/jotech/gapseq ``` Detailed information on [installation and troubleshooting](https://github.com/jotech/gapseq/blob/master/docs/install.md). +### Using Bioconda +Gapseq has a [bioconda](https://anaconda.org/bioconda/gapseq) package. You must have conda/miniconda/[miniforge](https://github.com/conda-forge/miniforge#install) installed already. +```bash +conda create -c conda-forge -c bioconda -c r -n gapseq gapseq +``` + ## Quickstart For detailed use cases and full tutorials, see the [documentation](https://gapseq.readthedocs.io/). From 30792cbeda770ec6f9df5ab30564c6d2b2ad2bef Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 24 Apr 2024 13:26:16 +0200 Subject: [PATCH 4/6] Add minor detail --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 06848c11..3ba7dcd0 100644 --- a/README.md +++ b/README.md @@ -33,6 +33,8 @@ Gapseq has a [bioconda](https://anaconda.org/bioconda/gapseq) package. You must conda create -c conda-forge -c bioconda -c r -n gapseq gapseq ``` +Hint: _When installing with bioconda, the gapseq binary will reside in your PATH, so you will not have to prepend "./" in front of gapseq. (Use "gapseq" instead of "./gapseq")._ + ## Quickstart For detailed use cases and full tutorials, see the [documentation](https://gapseq.readthedocs.io/). From 0c3c27f1398b7a4721f0db3e3ed668c828d230a4 Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Fri, 24 May 2024 15:56:25 +0200 Subject: [PATCH 5/6] r-chnosz moved to conda-forge https://github.com/conda-forge/staged-recipes/pull/26190 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3ba7dcd0..8e03ef99 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ Detailed information on [installation and troubleshooting](https://github.com/jo ### Using Bioconda Gapseq has a [bioconda](https://anaconda.org/bioconda/gapseq) package. You must have conda/miniconda/[miniforge](https://github.com/conda-forge/miniforge#install) installed already. ```bash -conda create -c conda-forge -c bioconda -c r -n gapseq gapseq +conda create -c conda-forge -c bioconda -n gapseq gapseq ``` Hint: _When installing with bioconda, the gapseq binary will reside in your PATH, so you will not have to prepend "./" in front of gapseq. (Use "gapseq" instead of "./gapseq")._ From bed56071b0c147e070abb1c3dbf45e6040f8639c Mon Sep 17 00:00:00 2001 From: "Carl M. Kobel" Date: Tue, 28 May 2024 14:40:12 +0200 Subject: [PATCH 6/6] change link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8e03ef99..75ea8d98 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # gapseq _Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks_ [![Documentation Status](https://readthedocs.org/projects/gapseq/badge/?version=latest)](https://gapseq.readthedocs.io/en/latest/?badge=latest) -[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) [![conda build](https://img.shields.io/conda/v/bioconda/gapseq)](https://bioconda.github.io/recipes/gapseq/README.html) +[![DOI:10.1186/s13059-021-02295-1](https://zenodo.org/badge/DOI/10.1186/s13059-021-02295-1.svg)](https://doi.org/10.1186/s13059-021-02295-1) [![conda build](https://img.shields.io/conda/v/bioconda/gapseq)](https://anaconda.org/bioconda/gapseq) _gapseq_ is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation.