From 2dece3147fad09850ce3906e4b9654f45e675c5a Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 14:47:32 +0200 Subject: [PATCH 01/11] intermediate kipoiseq version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8189643..a1cd8b9 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ requirements = [ 'setuptools', - 'kipoiseq>=0.7', + 'kipoiseq>=0.7,<0.8', 'cyvcf2', 'tensorflow', 'scipy', From 0aac5ccaaf7c73f7759274439f57f877008f595d Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:01:33 +0200 Subject: [PATCH 02/11] intermediate kipoiseq version --- .circleci/config.yml | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index c57111d..d7ab4b2 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,26 +6,18 @@ variables: run: name: Update conda command: | - conda install python=3.6 -y - conda update --yes conda - conda update setuptools - conda config --add channels bioconda - conda config --add channels conda-forge + conda env create -f environment.yaml install_mmsplice: &install_mmsplice run: name: Install mmsplice command: | - conda install cyvcf2 -y - conda install cython -y - conda install pybigwig -y pip install -e '.' - pip install pytest pytest-runner pytest-benchmark - install_dependencies: &install_dependencies - run: - name: Install dependencies not in miniconda3 - command: | - apt-get update && \ - apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev + # install_dependencies: &install_dependencies + # run: + # name: Install dependencies not in miniconda3 + # command: | + # apt-get update && \ + # apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev test_cli: &test_cli run: name: Test cli @@ -71,7 +63,7 @@ jobs: steps: - checkout - *update_conda - - *install_dependencies + # - *install_dependencies - *install_mmsplice - *test_cli - *run_tests From 42842400ce7a905d70370153dbde478a0b6d89d3 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:04:32 +0200 Subject: [PATCH 03/11] intermediate kipoiseq version --- .gitignore | 2 +- environment.yaml | 21 +++++++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 environment.yaml diff --git a/.gitignore b/.gitignore index b98c3fd..7cbca64 100644 --- a/.gitignore +++ b/.gitignore @@ -109,7 +109,7 @@ variant_effect_output.txt variant_effect_output.txt_summary.html variant_effect_output.txt_warnings.txt *-env/ -env* +# env* notebooks/pred.csv notebooks/pred_exon.csv tests/data/test-out.vcf diff --git a/environment.yaml b/environment.yaml new file mode 100644 index 0000000..bd60c0e --- /dev/null +++ b/environment.yaml @@ -0,0 +1,21 @@ +name: mmsplice_dev +channels: + - conda-forge + - bioconda +dependencies: + - 'python=3.7' + - 'cython' + - 'setuptools' + - 'kipoiseq>=0.7,<0.8' + - 'cyvcf2' + - 'tensorflow' + - 'scipy' + - 'pandas' + - 'pyfaidx' + - 'tqdm' + - 'click' + - 'pyranges>=0.0.71' + - 'pip' + - 'pytest' + - 'pytest-runner' + - 'pytest-benchmark' \ No newline at end of file From e4115c6d04089a2409c52860de0ac6093a1dabc6 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:06:16 +0200 Subject: [PATCH 04/11] activate env --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index d7ab4b2..23f6d9e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -7,6 +7,7 @@ variables: name: Update conda command: | conda env create -f environment.yaml + conda activate mmsplice_dev install_mmsplice: &install_mmsplice run: name: Install mmsplice From 207b6e0cf0a25d9aa8d53e92c1a64f9edcb9a429 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:12:44 +0200 Subject: [PATCH 05/11] use mamba --- .circleci/config.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 23f6d9e..90f43c7 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,7 +6,8 @@ variables: run: name: Update conda command: | - conda env create -f environment.yaml + conda install mamba + mamba env create -f environment.yaml conda activate mmsplice_dev install_mmsplice: &install_mmsplice run: From ed86e6ed40a1485dae1875e4dcefb31c367dc0b6 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:14:05 +0200 Subject: [PATCH 06/11] fix mamba --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 90f43c7..b9c4ebb 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,7 +6,7 @@ variables: run: name: Update conda command: | - conda install mamba + conda install -c conda-forge mamba -y mamba env create -f environment.yaml conda activate mmsplice_dev install_mmsplice: &install_mmsplice From a45c840485cf44cb0beb355c55976b049edd928b Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:18:40 +0200 Subject: [PATCH 07/11] use source activate --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b9c4ebb..d35ff36 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -8,7 +8,7 @@ variables: command: | conda install -c conda-forge mamba -y mamba env create -f environment.yaml - conda activate mmsplice_dev + source activate mmsplice_dev install_mmsplice: &install_mmsplice run: name: Install mmsplice From 95b2d837331b1a0cc431429ac8895bcb010673f5 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:25:20 +0200 Subject: [PATCH 08/11] install dependencies added --- .circleci/config.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d35ff36..66c3075 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -14,12 +14,12 @@ variables: name: Install mmsplice command: | pip install -e '.' - # install_dependencies: &install_dependencies - # run: - # name: Install dependencies not in miniconda3 - # command: | - # apt-get update && \ - # apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev + install_dependencies: &install_dependencies + run: + name: Install dependencies not in miniconda3 + command: | + apt-get update && \ + apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev test_cli: &test_cli run: name: Test cli @@ -65,7 +65,7 @@ jobs: steps: - checkout - *update_conda - # - *install_dependencies + - *install_dependencies - *install_mmsplice - *test_cli - *run_tests From 3905897fd324c458655dd2dfa036f62f8fddf154 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:37:44 +0200 Subject: [PATCH 09/11] activate env again --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 66c3075..d78538b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -27,7 +27,9 @@ variables: run_tests: &run_tests run: name: Run tests - command: pytest + command: | + source activate mmsplice_dev + pytest install_docker: &install_docker run: name: Install Docker client From 3399cf76da7a1c53e79247c93ee9676f2fb0f95c Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 15:44:28 +0200 Subject: [PATCH 10/11] activate env everywhere --- .circleci/config.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d78538b..b5bca6c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,17 +13,21 @@ variables: run: name: Install mmsplice command: | + source activate mmsplice_dev pip install -e '.' install_dependencies: &install_dependencies run: name: Install dependencies not in miniconda3 command: | + source activate mmsplice_dev apt-get update && \ apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev test_cli: &test_cli run: name: Test cli - command: mmsplice + command: | + source activate mmsplice_dev + mmsplice run_tests: &run_tests run: name: Run tests From 19b7f3a4efd996b387cd5d2e9f6129691046bfc1 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Tue, 18 Apr 2023 16:07:53 +0200 Subject: [PATCH 11/11] added pybigwig --- environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yaml b/environment.yaml index bd60c0e..a77d20d 100644 --- a/environment.yaml +++ b/environment.yaml @@ -5,6 +5,7 @@ channels: dependencies: - 'python=3.7' - 'cython' + - 'pybigwig' - 'setuptools' - 'kipoiseq>=0.7,<0.8' - 'cyvcf2'