From 50b5158c0b60f317fb36f269f035f2b6e979f470 Mon Sep 17 00:00:00 2001 From: Chris Myers Date: Mon, 11 Sep 2023 09:51:58 -0600 Subject: [PATCH 1/8] Update for release --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 2cdb1c0..10ef069 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -29,7 +29,7 @@ services: - backend=http://localhost:6789 - backendSS=http://synbiohubbackend:6789 synbiohub: - image: synbiohub/synbiohub:snapshot-standalone + image: synbiohub/synbiohub:1.6.1-standalone depends_on: - virtuoso ports: From ba2dd1d905b6c469bcfa699b69ca809c2f964692 Mon Sep 17 00:00:00 2001 From: Chris Myers Date: Mon, 11 Sep 2023 09:55:03 -0600 Subject: [PATCH 2/8] fix typo --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 494c735..5a99251 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ The base configuration, described with `docker-compose.yml`, is simply SynBioHub To run the base configuration: 1. Open terminal 2. `git clone https://github.com/synbiohub/synbiohub2-docker` -3. `docker-compose --f ./synbiohub2-docker/docker-compose.yml up` +3. `docker-compose -f ./synbiohub2-docker/docker-compose.yml up` ### With Explorer -To add [SBOLExplorer](https://github.com/michael13162/SBOLExplorer), add the `docker-compose.explorer.yml` to the main docker-compose, i.e. for step 3 run `docker-compose --f ./synbiohub2-docker/docker-compose.yml -f ./synbiohub2-docker/docker-compose.explorer.yml up` +To add [SBOLExplorer](https://github.com/michael13162/SBOLExplorer), add the `docker-compose.explorer.yml` to the main docker-compose, i.e. for step 3 run `docker-compose -f ./synbiohub2-docker/docker-compose.yml -f ./synbiohub2-docker/docker-compose.explorer.yml up` From 6b80b8d0c51f5588b8af9c9b6dfbb06dc080819c Mon Sep 17 00:00:00 2001 From: cjmyers Date: Mon, 11 Sep 2023 10:14:59 -0600 Subject: [PATCH 3/8] Update docker-compose.yml --- docker-compose.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 10ef069..409d13b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -26,8 +26,8 @@ services: dns: 8.8.8.8 restart: always environment: - - backend=http://localhost:6789 - - backendSS=http://synbiohubbackend:6789 + - backend=http://localhost:7777 + - backendSS=http://synbiohubbackend:7777 synbiohub: image: synbiohub/synbiohub:1.6.1-standalone depends_on: From b71378bb3232d7b1a4fda3dccd6b695ef530d6a5 Mon Sep 17 00:00:00 2001 From: cjmyers Date: Mon, 11 Sep 2023 10:20:59 -0600 Subject: [PATCH 4/8] Update docker-compose.yml --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 409d13b..34fbcf4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -27,7 +27,7 @@ services: restart: always environment: - backend=http://localhost:7777 - - backendSS=http://synbiohubbackend:7777 + - backendSS=http://synbiohub:7777 synbiohub: image: synbiohub/synbiohub:1.6.1-standalone depends_on: From cf80d4c94fe8a8f591602571639b2e3f2d95144d Mon Sep 17 00:00:00 2001 From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com> Date: Wed, 11 Sep 2024 11:02:59 -0600 Subject: [PATCH 5/8] virtuoso multiuser --- docker-compose.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index 34fbcf4..3328428 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -10,6 +10,11 @@ services: - /var/run/docker.sock:/var/run/docker.sock virtuoso: image: tenforce/virtuoso:virtuoso7.2.5 + environment: + - VIRT_SPARQL_MaxQueryCostEstimationTime=default + - VIRT_SPARQL_MaxQueryExecutionTime=300 + - VIRT_Parameters_ServerThreads=100 + - VIRT_HTTPServer_ServerThreads=100 volumes: - type: volume source: virtuoso-db1 From 4071e59f1bb91c3a70d55d2deada8f26d1399961 Mon Sep 17 00:00:00 2001 From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com> Date: Thu, 26 Sep 2024 15:36:22 -0600 Subject: [PATCH 6/8] Update docker-compose.yml --- docker-compose.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 3328428..8de2f6d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -13,8 +13,8 @@ services: environment: - VIRT_SPARQL_MaxQueryCostEstimationTime=default - VIRT_SPARQL_MaxQueryExecutionTime=300 - - VIRT_Parameters_ServerThreads=100 - - VIRT_HTTPServer_ServerThreads=100 + - VIRT_Parameters_ServerThreads=30 + - VIRT_HTTPServer_ServerThreads=300 volumes: - type: volume source: virtuoso-db1 From 60aea4de8260e467dfd47e1265171b36645c5c76 Mon Sep 17 00:00:00 2001 From: learner97 Date: Fri, 31 Jan 2025 16:58:41 -0700 Subject: [PATCH 7/8] changed virtuoso image --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index d8393b4..a223e3b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -9,7 +9,7 @@ services: volumes: - /var/run/docker.sock:/var/run/docker.sock virtuoso: - image: tenforce/virtuoso:virtuoso7.2.5 + image: askomics/virtuoso:7.2.14 volumes: - type: volume source: virtuoso-db1 From 3ddfd5d9bda6ce64d36fef12fe46b3d9af298bc2 Mon Sep 17 00:00:00 2001 From: Daniel Fang Date: Wed, 5 Feb 2025 11:39:19 -0700 Subject: [PATCH 8/8] Update docker-compose.yml --- docker-compose.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index ee4da6d..461406d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -13,8 +13,8 @@ services: environment: - VIRT_SPARQL_MaxQueryCostEstimationTime=default - VIRT_SPARQL_MaxQueryExecutionTime=300 - - VIRT_Parameters_ServerThreads=30 - - VIRT_HTTPServer_ServerThreads=300 + - VIRT_Parameters_ServerThreads=100 + - VIRT_HTTPServer_ServerThreads=100 volumes: - type: volume source: virtuoso-db1 @@ -34,7 +34,7 @@ services: - backend=http://localhost:7777 - backendSS=http://synbiohub:7777 synbiohub: - image: synbiohub/synbiohub:1.6.1-standalone + image: synbiohub/synbiohub:snapshot-standalone depends_on: - virtuoso ports: