From 0ab74c7c4e9cbf3458d23e3f01422819efdfaab1 Mon Sep 17 00:00:00 2001 From: Harriet Dashnow Date: Thu, 25 Feb 2021 15:59:01 -0700 Subject: [PATCH 1/2] add conda install instructions noting error message --- docs/source/install.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/source/install.rst b/docs/source/install.rst index e3373a1..02ddb50 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -22,6 +22,12 @@ We suggest conda installation if you want to perform outlier analysis, which req conda config --add channels bioconda conda install -y strling +The following should now be in your path: +`strling` +`strling-outliers.py` + +Note: It should be safe to ignore "Solving environment: failed ..." messages as long as the message "Solving environment: done" appears following the failed message and the install proceeds. + Install from source ------------------- From 6525f10c564fdc7220077aa52e06f789e51073be Mon Sep 17 00:00:00 2001 From: Harriet Dashnow Date: Fri, 26 Feb 2021 14:15:26 -0700 Subject: [PATCH 2/2] add link back to GitHub repo --- docs/source/index.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/index.rst b/docs/source/index.rst index 371dd6a..b54b07b 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,6 +6,8 @@ Welcome to STRling's documentation! =================================== +STRling code: https://github.com/quinlan-lab/STRling + STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data. It is capable of detecting novel STR expansions, that is expansions where there is no STR in the reference genome at that position (or a different repeat unit from what is in the reference). It can also detect STR expansions that are annotated in the reference genome. STRling uses kmer counting to recover mis-mapped STR reads. It then uses soft-clipped reads to precisely discover the position of the STR expansion in the reference genome. .. toctree::