From 1eb97d34ff2cb79345569a48f6c188b897cea4a9 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 8 Nov 2021 10:20:23 +0100 Subject: [PATCH 1/3] Update README.txt to switch to Markdown format Former-commit-id: 62b255841b6cb935edd9faef126eb1b133366df3 Former-commit-id: a9af4e20cc1b0bcdc01a45cb890dfee8b9b75a5c --- README.txt | 113 +++++++++++++++++++++++++++-------------------------- 1 file changed, 58 insertions(+), 55 deletions(-) diff --git a/README.txt b/README.txt index 816963f..ade0e48 100644 --- a/README.txt +++ b/README.txt @@ -1,57 +1,60 @@ -# -# ------------------------------------------ # ORG.Annot - Organelle Annotator -# version 1.0.0 - Sept 2015 -# ------------------------------------------ -# -# ------------------------- -# -1- Installation -# ------------------------- -# + +**version 1.0.0 - Sept 2015** + +## -1- Installation + # First check if binaries have been already compiled for your port -# -# $ scripts/check_port.sh -# -# if it prints : -# -# + checking port compilation OK -# -# then everything is fine -# -# if it prints : -# -# + port not yet compiled -# -# then, you should first compile binaries for your port -# please consult: src/README.txt for details -# -# if it prints smthing like -# * XXX version A.B.C (should be >= X.Y.Z) -# * please consider installing XXX from src/_unix_tools_ -# -# then, you should first compile some unix tools binaries for your port -# please consult: src/README.txt for details -# -# ------------------------- -# -2- Distribution organisation -# ------------------------- -# -# config : config file for (re)compiling tools -# data : internal data files (e.g. ChloroDB) -# detectors : features specific detector scripts -# ports : binaries for various ports -# scripts : main scripts directory -# src : sources for (re)compiling tools -# -# ------------------------- -# -3- Usage -# ------------------------- -# -# note: all scripts are located in scripts, so you may add -# this directory in your path -# e.g. using csh -# set path = ($path /scripts) -# -# @TODO : scripts description -# -# test + +```bash +scripts/check_port.sh +``` + +if it prints : + +``` +checking port compilation OK +``` + +then everything is fine + +if it prints : + +``` +port not yet compiled +``` + +then, you should first compile binaries for your port +please consult: src/README.txt for details + +if it prints something like + +``` +XXX version A.B.C (should be >= X.Y.Z) +please consider installing XXX from src/_unix_tools_ +``` + +then, you should first compile some unix tools binaries for your port +please consult: `src/README.txt` for details + +## -2- Distribution organisation + + +- config : config file for (re)compiling tools +- data : internal data files (e.g. ChloroDB) +- detectors : features specific detector scripts +- ports : binaries for various ports +- scripts : main scripts directory +- src : sources for (re)compiling tools + +## -3- Usage + + +> note: all scripts are located in scripts, so you may add +> this directory in your path +> e.g. using csh +> set path = ($path /scripts) + +@TODO : scripts description + +test From eb2bd2ce059810cd7224482c6516f68a966c6117 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 8 Nov 2021 10:21:06 +0100 Subject: [PATCH 2/3] Update README.txt name to `.md` Former-commit-id: 9b7bbd0431dbb98a7003291bf3964cac5a8b5b31 Former-commit-id: 78ea944e8e00fdfbb6ef0971aebbdbda0075828e --- README.txt => README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename README.txt => README.md (100%) diff --git a/README.txt b/README.md similarity index 100% rename from README.txt rename to README.md From 00454a529ec9a48427b83a4f15e2b330c8906090 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 8 Nov 2021 10:33:06 +0100 Subject: [PATCH 3/3] Update README.md to list every nix packages corresponding to org.annot dependences Former-commit-id: 12c47ebe65b3b3b5e89fea56d49b73d18217c853 Former-commit-id: f0236b1c6048df06b1d075ce2be0f4efc3e6c100 --- README.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/README.md b/README.md index ade0e48..51aa22d 100644 --- a/README.md +++ b/README.md @@ -58,3 +58,24 @@ please consult: `src/README.txt` for details @TODO : scripts description test + +## -4- Nix packages + +- `aragorn` : Version: 1.2.38 (maintainer Bruno Bzeznik) +- `clustalo` +- `exonerate` : Version: 2.4.0 (maintainer Bruno Bzeznik) +- `hmmer` : Version: 3.3.2 (maintainer Markus J. Ankenbrand) +- `kimono` +- `muscle` : Version: 3.8.31 (maintainer Renato Alves) +- `blast` : Version: 2.11.0 (maintainer Luis Pedro Coelho) +- `prokov` : +- `repseek` +- `sequtils` +- `sumaclust` : Version: 1.0.34 (maintainer Bruno Bzeznik) +- `sumatra` : Version: 1.0.34 (maintainer Bruno Bzeznik) +- `gawk` : Version: 5.1.0 +- `getopt` : Version: 1.1.6 +- `cd-hit` : Version: 4.8.1 (maintainer Bruno Bzeznik) +- `tcsh` : Version: 6.22.03 (maintainer Anderson Torres) +- `ITSx` : Version: 1.1.1 (maintainer Anderson Torres) +