From 11ae52b81cdf0f4647750f088efa626c30d3a6dd Mon Sep 17 00:00:00 2001 From: Victoire BAILLET <victoire.baillet@pasteur.fr> Date: Wed, 19 Apr 2023 18:19:30 +0200 Subject: [PATCH] def path to wrappers (update readme) --- README.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 473fe56c..1445b361 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,6 @@ [](https://gitlab.pasteur.fr/hub/cc-qtl-db/commits/dev) [](https://gitlab.pasteur.fr/hub/cc-qtl-db/commits/dev) -<!-- Take a look at its [wiki](https://gitlab.pasteur.fr/hub/cc-qtl-db/wikis/home) --> - [[_TOC_]] ## Introduction @@ -336,7 +334,7 @@ The analysis parameters, however, are not compatible with two-way RIL (namely, a One key feature of CC-QTL is that given its database structure, it is thought in such a way that phenotypic data can be acquired for multiple traits, over different experiments performed by different users, with the objective in the long run to assess traits correlations. That requires the mouse genotypes to be reproducible, which is the case for CC lines, but not for DO lines, another mouse multiparental mapping population deriving from the same 8 founder lines than the CC, in which by design each line has a unique genetic makeup which cannot be reproduced. -Ongoing work on CC-QTL (medium term objective) is to extend it to so-called CC-RIX, which are intercrosses between CC lines. CC-RIX are genetically reproducible like CCs, yet benefit from the buffering effect of heterozygosity and allow to assess parental effects. +Ongoing work on CC-QTL is to extend it to so-called CC-RIX, which are intercrosses between CC lines. CC-RIX are genetically reproducible like CCs, yet benefit from the buffering effect of heterozygosity and allow to assess parental effects. ### How can I install the analysis workflow on Galaxy ? @@ -344,7 +342,7 @@ We made the analysis workflow Galaxy-powered to both guarantee reproducibility a In case you are solely interested in deploying and running CC-QTL locally on your computer, eg for test purposes, nothing is required from your side else than following the installation instructions, as the Docker will deploy a local Galaxy along with all the interface components. -If you want, however, to install it on a pre-existing Galaxy instance (eg, Galaxy instance from your institute): you can do so using the [wrappers](path to wrappers) we use on the Galaxy@Pasteur instance. The current version of CC-QTL is indeed not yet compatible for an installation using the Galaxy Toolshed (this will be the case from the next release onwards). +If you want, however, to install it on a pre-existing Galaxy instance (eg, Galaxy instance from your institute): you can do so using the [wrappers](https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/cc_qtl) we use on the Galaxy@Pasteur instance. The current version of CC-QTL is indeed not yet compatible for an installation using the Galaxy Toolshed, this will be the case from the next release onwards. Keep in mind, though, that by using CC-QTL directly through Galaxy, you will get the analysis workflow yet not the database, nor the interface ; thus not benefiting from all the functionalities of CC-QTL (eg plots). -- GitLab