From d8a80d01c34641b16743e0f9acc343543677cb34 Mon Sep 17 00:00:00 2001 From: claudiofr Date: Thu, 17 Aug 2023 14:11:42 -0400 Subject: [PATCH 1/3] Support genome browser chain file format. Support a new datatype for the genome browser chain file format described here: https://genome.ucsc.edu/goldenPath/help/chain.html Add meta data which lists the number of chains in the file and a sniffer for auto-detecting the chain format. --- .../config/sample/datatypes_conf.xml.sample | 2 + lib/galaxy/datatypes/chain.py | 124 + lib/galaxy/datatypes/test/1.chain | 55552 ++++++++++++++++ lib/galaxy/datatypes/test/2.chain | 50184 ++++++++++++++ 4 files changed, 105862 insertions(+) create mode 100644 lib/galaxy/datatypes/chain.py create mode 100755 lib/galaxy/datatypes/test/1.chain create mode 100755 lib/galaxy/datatypes/test/2.chain diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index 3a0aab6f6a15..9f913870fe55 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -960,6 +960,7 @@ +