From 5f04309e61c9acb531dcff8eb6bc276320d67a4c Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Thu, 16 May 2024 14:45:51 +0100 Subject: [PATCH 1/2] extend chmod of STAR directory to use g-s --- data/vtlib/star_alignment.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/star_alignment.json b/data/vtlib/star_alignment.json index a0c2fa696..7d374c3b4 100644 --- a/data/vtlib/star_alignment.json +++ b/data/vtlib/star_alignment.json @@ -291,7 +291,7 @@ "type":"EXEC", "use_STDIN": false, "use_STDOUT": false, - "cmd":[ "chmod", "-R", "g+w", {"port":"src_stargenome_dir", "direction":"in"} ], + "cmd":[ "chmod", "-R", "g+w,g-s", {"port":"src_stargenome_dir", "direction":"in"} ], "comment":"This is necessary because STAR creates this transitional directory as group-read-only and cannot be deleted later" }, { From 05b9eaca949a2e9f1f6123eb4cd571cb89763e58 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Wed, 5 Jun 2024 16:44:38 +0100 Subject: [PATCH 2/2] make chmod add g+rwx permissions (instead of just g+w) --- data/vtlib/star_alignment.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/star_alignment.json b/data/vtlib/star_alignment.json index 7d374c3b4..283deb9b0 100644 --- a/data/vtlib/star_alignment.json +++ b/data/vtlib/star_alignment.json @@ -291,7 +291,7 @@ "type":"EXEC", "use_STDIN": false, "use_STDOUT": false, - "cmd":[ "chmod", "-R", "g+w,g-s", {"port":"src_stargenome_dir", "direction":"in"} ], + "cmd":[ "chmod", "-R", "g+rwx,g-s", {"port":"src_stargenome_dir", "direction":"in"} ], "comment":"This is necessary because STAR creates this transitional directory as group-read-only and cannot be deleted later" }, {