From 71234b0f95869d7fad4f81cb521ba83787d7f48b Mon Sep 17 00:00:00 2001
From: NickKolok <nickkolok@mail.ru>
Date: Tue, 28 Jan 2025 16:57:59 +0300
Subject: [PATCH] [minor] Replace `theaidenlab` with `aidenlab`
As for now, github.com/theaidenlab redirects to github.com/aidenlab .
However, we should not rely on the redirect, and fix it advance.
Just is case. Just for consistency.
---
AWS/README.md | 4 ++--
CPU/README.md | 4 ++--
Docker/install-dependencies.sh | 4 ++--
LSF/README.md | 2 +-
README.md | 4 ++--
SLURM/README.md | 2 +-
UGER/README.md | 2 +-
7 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/AWS/README.md b/AWS/README.md
index 75d8a92..ced2150 100755
--- a/AWS/README.md
+++ b/AWS/README.md
@@ -1,2 +1,2 @@
-Extensive instructions, including how to create and launch an instance, are
-available [on the wiki](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-Amazon-Web-Services)
+Extensive instructions, including how to create and launch an instance, are
+available [on the wiki](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-Amazon-Web-Services)
diff --git a/CPU/README.md b/CPU/README.md
index f6658c3..6416301 100644
--- a/CPU/README.md
+++ b/CPU/README.md
@@ -4,6 +4,6 @@
Report bugs using the Issues tab.
-Follow the documentation on [the wiki](https://github.com/theaidenlab/juicer/wiki/Installation) for dependencies, directory structure, and usage.
+Follow the documentation on [the wiki](https://github.com/aidenlab/juicer/wiki/Installation) for dependencies, directory structure, and usage.
-**PLEASE NOTE:** The CPU version is fine for small Hi-C experiments, but any reasonably sized experiment will take an extremely long time to run and therefore should be run [on a cluster](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-a-cluster) or [in the cloud](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-Amazon-Web-Services).
+**PLEASE NOTE:** The CPU version is fine for small Hi-C experiments, but any reasonably sized experiment will take an extremely long time to run and therefore should be run [on a cluster](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-a-cluster) or [in the cloud](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-Amazon-Web-Services).
diff --git a/Docker/install-dependencies.sh b/Docker/install-dependencies.sh
index 8a8dc2b..b97bf47 100644
--- a/Docker/install-dependencies.sh
+++ b/Docker/install-dependencies.sh
@@ -50,8 +50,8 @@ curl -OL "https://github.com/4dn-dcic/pairix/archive/${PAIRIX_VERSION}.zip" && \
rm -rf "${PAIRIX_VERSION}.zip" "pairix-${PAIRIX_VERSION}"
# Install Juicer
-git clone --branch encode https://github.com/theaidenlab/juicer.git && \
- chmod +x juicer/CPU/* juicer/CPU/common/* juicer/misc/*
+git clone --branch encode https://github.com/aidenlab/juicer.git && \
+ chmod +x juicer/CPU/* juicer/CPU/common/* juicer/misc/*
# && \
# find -mindepth 1 -maxdepth 1 -type d -not -name "CPU" -not -name ".git" -not -name "misc" | xargs rm -rf
diff --git a/LSF/README.md b/LSF/README.md
index 6a51d20..793aaa3 100644
--- a/LSF/README.md
+++ b/LSF/README.md
@@ -6,4 +6,4 @@
We do not use LSF in our lab. We welcome other developers to update the LSF version to be consistent with the AWS LSF-like version.
-Report bugs using the Issues tab. See the [documentation on the wiki](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-a-cluster) to understand how to install and run Juicer.
+Report bugs using the Issues tab. See the [documentation on the wiki](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-a-cluster) to understand how to install and run Juicer.
diff --git a/README.md b/README.md
index c7af159..728e4ea 100755
--- a/README.md
+++ b/README.md
@@ -101,7 +101,7 @@ Instructions for installing the latest version of CUDA can be found on the
The native libraries included with Juicer are compiled for CUDA 7 or CUDA 7.5.
See the [download page for Juicer
-Tools](https://github.com/theaidenlab/juicer/wiki/Download).
+Tools](https://github.com/aidenlab/juicer/wiki/Download).
Other versions of CUDA can be used, but you will need to download the
respective native libraries from
@@ -115,7 +115,7 @@ If you cannot access a GPU, you can run the [CPU version of HiCCUPS](https://git
### Building new jars
-See the Juicebox documentation at <https://github.com/theaidenlab/Juicebox> for
+See the Juicebox documentation at <https://github.com/aidenlab/Juicebox> for
details on building new jars of the juicer_tools.
------------
diff --git a/SLURM/README.md b/SLURM/README.md
index f1b95bc..fd81add 100755
--- a/SLURM/README.md
+++ b/SLURM/README.md
@@ -1 +1 @@
-Please see the [wiki](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-a-cluster) for extensive instructions
+Please see the [wiki](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-a-cluster) for extensive instructions
diff --git a/UGER/README.md b/UGER/README.md
index f1b95bc..fd81add 100755
--- a/UGER/README.md
+++ b/UGER/README.md
@@ -1 +1 @@
-Please see the [wiki](https://github.com/theaidenlab/juicer/wiki/Running-Juicer-on-a-cluster) for extensive instructions
+Please see the [wiki](https://github.com/aidenlab/juicer/wiki/Running-Juicer-on-a-cluster) for extensive instructions