From b714d5d019dfbefc64fbcd5fe65ef51ab61e2c46 Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Thu, 15 Dec 2022 18:47:22 +0000 Subject: [PATCH 1/6] Get rid of all submodules --- .gitmodules | 9 --------- bwa | 1 - fermi-lite | 1 - 3 files changed, 11 deletions(-) delete mode 160000 bwa delete mode 160000 fermi-lite diff --git a/.gitmodules b/.gitmodules index 0f131ca11..e69de29bb 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,9 +0,0 @@ -[submodule "fermi-lite"] - path = fermi-lite - url = https://github.com/walaj/fermi-lite -[submodule "htslib"] - path = htslib - url = https://github.com/samtools/htslib -[submodule "bwa"] - path = bwa - url = https://github.com/walaj/bwa diff --git a/bwa b/bwa deleted file mode 160000 index 609311b88..000000000 --- a/bwa +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 609311b8842244c5c15405b3ea553455f542f786 diff --git a/fermi-lite b/fermi-lite deleted file mode 160000 index 5bc90f8d7..000000000 --- a/fermi-lite +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 5bc90f8d70e2b66184eccbd223a3be714c914365 From 8ad09a7c11d01b9496406ce642a0562bc2d733b8 Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Thu, 15 Dec 2022 18:48:10 +0000 Subject: [PATCH 2/6] Add updated fermi-lite submodule --- .gitmodules | 3 +++ fermi-lite | 1 + 2 files changed, 4 insertions(+) create mode 160000 fermi-lite diff --git a/.gitmodules b/.gitmodules index e69de29bb..1288325d6 100644 --- a/.gitmodules +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "fermi-lite"] + path = fermi-lite + url = git@github.com:julianhess/fermi-lite.git diff --git a/fermi-lite b/fermi-lite new file mode 160000 index 000000000..66e4b6fa7 --- /dev/null +++ b/fermi-lite @@ -0,0 +1 @@ +Subproject commit 66e4b6fa72c1cd97d78e3b678e780ff95ce9e039 From a26830bd5d2f84b427a3ea3e824ec5e2d5633872 Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Thu, 15 Dec 2022 18:59:02 +0000 Subject: [PATCH 3/6] Update BWA submodule --- .gitmodules | 3 +++ bwa | 1 + 2 files changed, 4 insertions(+) create mode 160000 bwa diff --git a/.gitmodules b/.gitmodules index 1288325d6..27b24e7b5 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,6 @@ [submodule "fermi-lite"] path = fermi-lite url = git@github.com:julianhess/fermi-lite.git +[submodule "bwa"] + path = bwa + url = git@github.com:lh3/bwa.git diff --git a/bwa b/bwa new file mode 160000 index 000000000..139f68fc4 --- /dev/null +++ b/bwa @@ -0,0 +1 @@ +Subproject commit 139f68fc4c3747813783a488aef2adc86626b01b From f9c934e55b54c9c3d5475b64cef411a9b89394c3 Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Thu, 15 Dec 2022 18:59:14 +0000 Subject: [PATCH 4/6] Update fermi-lite submodule again We can't use Heng Li's latest, since Jeremiah made some changes to it. --- fermi-lite | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fermi-lite b/fermi-lite index 66e4b6fa7..4e79d82b8 160000 --- a/fermi-lite +++ b/fermi-lite @@ -1 +1 @@ -Subproject commit 66e4b6fa72c1cd97d78e3b678e780ff95ce9e039 +Subproject commit 4e79d82b85d2e5d41c207399419b69df835bef93 From fc6b806373d31a48647528fb56ad88819eff7add Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Tue, 23 Jan 2024 13:31:14 +0000 Subject: [PATCH 5/6] Use https for submodules, so that SSH keys aren't required to clone --- .gitmodules | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index 27b24e7b5..1beea4569 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,6 @@ [submodule "fermi-lite"] path = fermi-lite - url = git@github.com:julianhess/fermi-lite.git + url = https://github.com/julianhess/fermi-lite.git [submodule "bwa"] path = bwa - url = git@github.com:lh3/bwa.git + url = https://github.com/lh3/bwa.git From 0a545148ac42f9ee00c64591ad7f3d6d76859da5 Mon Sep 17 00:00:00 2001 From: Julian Hess Date: Fri, 9 Aug 2024 19:56:55 +0000 Subject: [PATCH 6/6] Bump bwa/fermi submodules --- bwa | 2 +- fermi-lite | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bwa b/bwa index 139f68fc4..740d895fd 160000 --- a/bwa +++ b/bwa @@ -1 +1 @@ -Subproject commit 139f68fc4c3747813783a488aef2adc86626b01b +Subproject commit 740d895fd98893bd05fe6cbf765b9d2e93f92323 diff --git a/fermi-lite b/fermi-lite index 4e79d82b8..ec0b8b327 160000 --- a/fermi-lite +++ b/fermi-lite @@ -1 +1 @@ -Subproject commit 4e79d82b85d2e5d41c207399419b69df835bef93 +Subproject commit ec0b8b32787c05f97ca06157070dd49d9bdfa855