From da43789783532653493d59aac17a8f78851f9e2c Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 7 Oct 2024 15:54:02 +0100 Subject: [PATCH] ext-tools: add pydnatic --- opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile | 2 +- .../app/cli/main/options/AnalysisVariantCommandOptions.java | 4 ++-- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../org/opencb/opencga/client/rest/clients/VariantClient.java | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/python/pyopencga/rest_clients/variant_client.py | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile b/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile index 9b200a844b..c7cfcd9b69 100644 --- a/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile +++ b/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile @@ -14,9 +14,9 @@ RUN apt-get update -y && \ libssl-dev libssh-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \ gnuplot pandoc samtools bcftools tabix fastqc plink1.9 bwa r-base wget libopenblas0-openmp libcholmod3 libsuitesparse-dev && \ apt-get remove libopenblas0-pthread && \ + pip3 install pydantic && \ ## 2. Install samtools and bcftools 1.21 and plugins -# apt-get update -y && apt-get install -y wget && \ wget https://github.com/samtools/samtools/releases/download/1.21/samtools-1.21.tar.bz2 && \ tar xjvf samtools-1.21.tar.bz2 && \ cd samtools-1.21 && \ diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java index 2d55a799c5..3c1c4df251 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java @@ -1486,10 +1486,10 @@ public class RunLiftoverCommandOptions { @Parameter(names = {"--files"}, description = "List of VCF files to lift over", required = false, arity = 1) public String files; - @Parameter(names = {"--target-assembly"}, description = "Target assembly for lift over. Valid values: GRCh38 (for Ensembl) or hg38 (for NCBI)", required = false, arity = 1) + @Parameter(names = {"--target-assembly"}, description = "Target assembly for lift over. Valid values: GRCH38 (for Ensembl) or HG38 (for NCBI)", required = false, arity = 1) public String targetAssembly; - @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword OPENCGA_VCF_INPUT_FOLDER is used, they will be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1) + @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword OPENCGA_VCF_INPUT_FOLDER is used, then VCF files be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1) public String vcfDestination; @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1) diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 3039792780..664ee9c389 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -389,7 +389,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N #' @param jobScheduledStartTime Time when the job is scheduled to start. #' @param jobPriority Priority of the job. #' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run. - #' @param data BCFtools +liftover plugin parameterss. + #' @param data BCFtools +liftover plugin parameters. runLiftover=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="variant/liftover", subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 4c68a7f4da..b25522bd3c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -552,7 +552,7 @@ public RestResponse runKnockout(KnockoutAnalysisParams data, ObjectMap para /** * BCFtools liftover plugin maps coordinates from assembly 37 to 38. - * @param data BCFtools +liftover plugin parameterss. + * @param data BCFtools +liftover plugin parameters. * @param params Map containing any of the following optional parameters. * study: study. * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index 828a0664be..131a93891e 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -445,7 +445,7 @@ export default class Variant extends OpenCGAParentClass { } /** BCFtools liftover plugin maps coordinates from assembly 37 to 38. - * @param {Object} data - BCFtools +liftover plugin parameterss. + * @param {Object} data - BCFtools +liftover plugin parameters. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - study. * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index a9eff0ce62..01b79bbefa 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -575,7 +575,7 @@ def run_liftover(self, data=None, **options): BCFtools liftover plugin maps coordinates from assembly 37 to 38. PATH: /{apiVersion}/analysis/variant/liftover/run - :param dict data: BCFtools +liftover plugin parameterss. (REQUIRED) + :param dict data: BCFtools +liftover plugin parameters. (REQUIRED) :param str study: study. :param str job_id: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.