From b7d4be7a5f0ca36c40385492a725dccee1ddd70d Mon Sep 17 00:00:00 2001 From: bio-boris Date: Thu, 8 May 2025 12:06:25 -0500 Subject: [PATCH 1/5] Update kb_SPAdesImpl.py --- lib/kb_SPAdes/kb_SPAdesImpl.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/kb_SPAdes/kb_SPAdesImpl.py b/lib/kb_SPAdes/kb_SPAdesImpl.py index fa1bd16..f5a733d 100644 --- a/lib/kb_SPAdes/kb_SPAdesImpl.py +++ b/lib/kb_SPAdes/kb_SPAdesImpl.py @@ -81,8 +81,8 @@ class kb_SPAdes: MAX_THREADS_META = 128 # Increase threads for metagenomic assemblies MEMORY_OFFSET_GB = 1 # 1GB MIN_MEMORY_GB = 4 - MAX_MEMORY_GB_SPADES = 500 - MAX_MEMORY_GB_META_SPADES = 1000 + MAX_MEMORY_GB_SPADES = 200 + MAX_MEMORY_GB_META_SPADES = 490 GB = 1000000000 URL_WS = 'workspace-url' From 7cce665a524ec31cd2acb1a22a91f0009b131bfd Mon Sep 17 00:00:00 2001 From: bio-boris Date: Thu, 8 May 2025 12:08:59 -0500 Subject: [PATCH 2/5] Update kb_sdk_test.yaml --- .github/workflows/kb_sdk_test.yaml | 79 ++++++++++-------------------- 1 file changed, 25 insertions(+), 54 deletions(-) diff --git a/.github/workflows/kb_sdk_test.yaml b/.github/workflows/kb_sdk_test.yaml index a31e626..1c67b63 100644 --- a/.github/workflows/kb_sdk_test.yaml +++ b/.github/workflows/kb_sdk_test.yaml @@ -1,62 +1,33 @@ -name: KBase SDK Tests +name: Run KBase SDK Tests on: push: - branches: - - master - - main pull_request: - branches: - - master - - main - - develop jobs: - - sdk_tests: + test: runs-on: ubuntu-latest - steps: - - - name: Check out GitHub repo - if: "!contains(github.event.head_commit.message, 'skip ci')" - uses: actions/checkout@v2 - - - name: Check out Actions CI files - if: "!contains(github.event.head_commit.message, 'skip ci')" - uses: actions/checkout@v2 - with: - repository: 'kbaseapps/kb_sdk_actions' - path: 'kb_sdk_actions' - - - name: Set up test environment - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} - run: | - # Verify kb_sdk_actions clone worked - test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned" - # Pull kb-sdk & create startup script - docker pull kbase/kb-sdk - - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local" - test -f "test_local/test.cfg" && echo "Confirmed config exists" - - - name: Configure authentication - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} - run: | - # Add token to config - sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg - - - name: Run tests - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - run: | - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test - bash <(curl -s https://codecov.io/bash) + steps: + - uses: actions/checkout@v4 + + - name: Download kb-sdk, set up path, and modify kb-sdk helper script + run: | + mkdir -p $(pwd)/bin + docker run ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 genscript > $(pwd)/bin/kb-sdk + docker tag ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 kbase/kb-sdk:latest + chmod 755 $(pwd)/bin/kb-sdk + echo "$(pwd)/bin" >> $GITHUB_PATH + sed -i 's/docker run -it/docker run /g' $(pwd)/bin/kb-sdk + + - name: Setup KBase SDK Tests and inject kbase token + env: + KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} + run: | + kb-sdk test || true + mkdir -p ./test_local + sed -i "s/^test_token=.*$/test_token=$KBASE_TEST_TOKEN/g" ./test_local/test.cfg + continue-on-error: true + + - name: Run KBase SDK Tests + run: kb-sdk test From 722a29aa24ea2b5d3c1e16d4462dc4d78f3fe73d Mon Sep 17 00:00:00 2001 From: bio-boris Date: Thu, 8 May 2025 12:12:56 -0500 Subject: [PATCH 3/5] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 834b779..28c30ac 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM kbase/sdkbase2:python +FROM kbase/sdkpython:3.8.0 MAINTAINER KBase Developer # ----------------------------------------- # In this section, you can install any system dependencies required From f67c75ceec20e11edd377426defba05e6e402bbc Mon Sep 17 00:00:00 2001 From: bio-boris Date: Thu, 8 May 2025 12:18:18 -0500 Subject: [PATCH 4/5] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 28c30ac..e44dd66 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,7 +20,7 @@ RUN pip install --upgrade pip \ ENV SPADES_VERSION='3.15.3' RUN cd /opt \ - && wget http://cab.spbu.ru/files/release${SPADES_VERSION}/SPAdes-${SPADES_VERSION}-Linux.tar.gz \ + && wget https://github.com/ablab/spades/releases/download/v3.15.3/SPAdes-3.15.3-Linux.tar.gz \ && tar -xvzf SPAdes-${SPADES_VERSION}-Linux.tar.gz \ && rm SPAdes-${SPADES_VERSION}-Linux.tar.gz From ec4aadbff8d443486086995f7e605507460524de Mon Sep 17 00:00:00 2001 From: crockettz Date: Mon, 28 Jul 2025 14:53:01 -0400 Subject: [PATCH 5/5] Added missing packages to dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e44dd66..7908e41 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN apt-get update \ && apt-get -y install gcc RUN pip install --upgrade pip \ - && pip3 install psutil \ + && pip3 install psutil numpy pyyaml \ && python --version ENV SPADES_VERSION='3.15.3'