From a956e0503b1b35eada1d6c051209495b93a6d93c Mon Sep 17 00:00:00 2001 From: Mikael Salson Date: Wed, 26 Jan 2022 12:56:24 +0100 Subject: [PATCH] doc/vidjil-algo.md: vidjil.org from http to https --- doc/vidjil-algo.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/vidjil-algo.md b/doc/vidjil-algo.md index 536dfd2ad..cf826ae49 100644 --- a/doc/vidjil-algo.md +++ b/doc/vidjil-algo.md @@ -14,11 +14,11 @@ This is the help of vidjil-algo, for command-line usage. This manual can be browsed online: - - (last stable release) + - (last stable release) - (development version) Other documentations for life scientists, bioinformaticians, server administrators, and developers -can be found ats . +can be found at . ## About @@ -27,7 +27,7 @@ can be found ats . diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. -With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus), +With adapted [library preparation and sequencing](https://www.vidjil.org/doc/locus), high-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated sequencing methods and software, called either Rep-Seq or AIRR-Seq. @@ -92,10 +92,10 @@ To compile Vidjil-algo, make sure: ### Download -These instructions target *stable releases* of vidjil-algo, as downloaded from . +These instructions target *stable releases* of vidjil-algo, as downloaded from . ``` sh -curl -O http://www.vidjil.org/releases/vidjil-algo-latest.tar.gz +curl -O https://www.vidjil.org/releases/vidjil-algo-latest.tar.gz tar xvfz vidjil-algo-latest.tar.gz cd vidjil-algo-* ``` @@ -121,7 +121,7 @@ make germline make -C src # build vijil-algo from the sources (see the requirements, - # another option is: wget http://www.vidjil.org/releases/vidjil-algo-latest_x86_64 -O vidjil-algo + # another option is: wget https://www.vidjil.org/releases/vidjil-algo-latest_x86_64 -O vidjil-algo # to download a static binary (built for x86_64 architectures) make demo # download demo files (S22 and L4, see demo/get-sequences) @@ -156,7 +156,7 @@ make -C src test # run self-tests (can take 5 to 60 minutes) Run the following commands: ``` sh -curl http://www.vidjil.org/releases/vidjil-algo-latest_x86_64 -o vidjil-algo +curl https://www.vidjil.org/releases/vidjil-algo-latest_x86_64 -o vidjil-algo chmod 755 vidjil-algo curl -O https://gitlab.inria.fr/vidjil/vidjil/-/raw/master/doc/vidjil-algo.md @@ -594,7 +594,7 @@ The default output of Vidjil-algo (with the default `-c clones` command) are the The web application takes this `.vidjil` file ([possibly merged with `fuse.py`](#following-clones-in-several-samples)) for the *visualization and analysis* of clones and their tracking along different samples (for example time points in a MRD setup or in a immunological study). - Please see the [web application user manual](http://www.vidjil.org/doc/user) for more information. + Please see the [web application user manual](https://www.vidjil.org/doc/user) for more information. - The `.tsv` file is the AIRR output, for compatibility with other software using the same format. See [below](#airr-tsv-output) for details. @@ -752,7 +752,7 @@ When processing large datasets, such as RNA-Seq or capture, one may want to pre- In such a case, the recommanded option is to use the `--filter-reads` preset, that launches Vidjil-algo without clone clustering and analysis, while outputing a `out/basename.detected.vdj.fa` file. This file contains reads /that may have V(D)J recombinations/, evaluated with a very permissive threshold. The resulting file is usually much smaller on such datasets and can then be transferred or analysed in-depth more easily. -This filtering can also be part of a [post-sequencer workflow](http://www.vidjil.org/doc/workflow/). +This filtering can also be part of a [post-sequencer workflow](https://www.vidjil.org/doc/workflow/). ## AIRR .tsv output -- GitLab