From 87c73201ff58f36e4ac5f276b97491b95cd219ec Mon Sep 17 00:00:00 2001 From: kaw97 <31460812+kaw97@users.noreply.github.com> Date: Tue, 2 Aug 2022 14:26:51 -0500 Subject: [PATCH 1/3] force scipy==1.8 --- autometa-env.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/autometa-env.yml b/autometa-env.yml index 6d195d2fb..cb614d817 100644 --- a/autometa-env.yml +++ b/autometa-env.yml @@ -23,6 +23,7 @@ dependencies: - rsync - samtools>=1.11 - scikit-bio + - scipy==1.8 #force scipy 1.8 until scikit-bio updates to 1.9, https://github.com/KwanLab/Autometa/issues/285 - scikit-learn==0.24 # prevent error from joblib in multiprocessing distance calculations - tqdm - trimap From 556c48b811f4a9d1dbf9133f69e06c14cab4247f Mon Sep 17 00:00:00 2001 From: kaw97 <31460812+kaw97@users.noreply.github.com> Date: Tue, 20 Sep 2022 13:14:46 -0500 Subject: [PATCH 2/3] update dockerfile --- docs/Dockerfile | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 docs/Dockerfile diff --git a/docs/Dockerfile b/docs/Dockerfile new file mode 100644 index 000000000..20514e8aa --- /dev/null +++ b/docs/Dockerfile @@ -0,0 +1,10 @@ +#Dockerfile for documentation +# +# +# +# + +FROM sphinxdoc/sphinx +WORKDIR /docs +ADD requirements.txt /docs +RUN pip3 install -r requirements.txt From 585bdc7aca038399b6dc0c51a522fa37672dfbae Mon Sep 17 00:00:00 2001 From: Kyle Wolf <31460812+kaw97@users.noreply.github.com> Date: Thu, 23 Mar 2023 14:30:31 -0500 Subject: [PATCH 3/3] replaced sample galaxy autometa images with the specific path to autometa 2.2 --- modules/local/align_reads.nf | 2 +- modules/local/binning.nf | 2 +- modules/local/binning_summary.nf | 2 +- modules/local/hmmer_hmmsearch_filter.nf | 2 +- modules/local/length_table.nf | 2 +- modules/local/majority_vote.nf | 2 +- modules/local/markers.nf | 2 +- modules/local/prepare_lca.nf | 2 +- modules/local/reduce_lca.nf | 2 +- modules/local/spades_kmer_coverage.nf | 2 +- modules/local/split_kingdoms.nf | 2 +- modules/local/unclustered_recruitment.nf | 2 +- subworkflows/local/prepare_ncbi_taxinfo.nf | 2 +- subworkflows/local/prepare_nr.nf | 4 ++-- 14 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/local/align_reads.nf b/modules/local/align_reads.nf index 1a5fd618e..472a8a25f 100644 --- a/modules/local/align_reads.nf +++ b/modules/local/align_reads.nf @@ -15,7 +15,7 @@ process ALIGN_READS { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/binning.nf b/modules/local/binning.nf index a8b9ebba3..877a65014 100644 --- a/modules/local/binning.nf +++ b/modules/local/binning.nf @@ -11,7 +11,7 @@ process BINNING { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/binning_summary.nf b/modules/local/binning_summary.nf index 18c1e1d27..66f377fca 100644 --- a/modules/local/binning_summary.nf +++ b/modules/local/binning_summary.nf @@ -12,7 +12,7 @@ process BINNING_SUMMARY { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/hmmer_hmmsearch_filter.nf b/modules/local/hmmer_hmmsearch_filter.nf index a21be8b3a..26d1d8cee 100644 --- a/modules/local/hmmer_hmmsearch_filter.nf +++ b/modules/local/hmmer_hmmsearch_filter.nf @@ -24,7 +24,7 @@ process HMMER_HMMSEARCH_FILTER { conda (params.enable_conda ? "autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/length_table.nf b/modules/local/length_table.nf index d6b95de69..a94c76833 100644 --- a/modules/local/length_table.nf +++ b/modules/local/length_table.nf @@ -12,7 +12,7 @@ process LENGTH_TABLE { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/majority_vote.nf b/modules/local/majority_vote.nf index 0d85eb4f2..7cd7bb218 100644 --- a/modules/local/majority_vote.nf +++ b/modules/local/majority_vote.nf @@ -12,7 +12,7 @@ process MAJORITY_VOTE { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/markers.nf b/modules/local/markers.nf index 5f458ad8b..5835735b7 100644 --- a/modules/local/markers.nf +++ b/modules/local/markers.nf @@ -13,7 +13,7 @@ process MARKERS { conda (params.enable_conda ? "autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/prepare_lca.nf b/modules/local/prepare_lca.nf index d8e4481d9..5d4de5e39 100644 --- a/modules/local/prepare_lca.nf +++ b/modules/local/prepare_lca.nf @@ -10,7 +10,7 @@ process PREPARE_LCA { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/reduce_lca.nf b/modules/local/reduce_lca.nf index 7d9a46930..28be0aaa1 100644 --- a/modules/local/reduce_lca.nf +++ b/modules/local/reduce_lca.nf @@ -12,7 +12,7 @@ process REDUCE_LCA { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/spades_kmer_coverage.nf b/modules/local/spades_kmer_coverage.nf index 6e803c6ef..5f36cc335 100644 --- a/modules/local/spades_kmer_coverage.nf +++ b/modules/local/spades_kmer_coverage.nf @@ -12,7 +12,7 @@ process SPADES_KMER_COVERAGE { conda (params.enable_conda ? "autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/split_kingdoms.nf b/modules/local/split_kingdoms.nf index 393d9504c..aa1f82059 100644 --- a/modules/local/split_kingdoms.nf +++ b/modules/local/split_kingdoms.nf @@ -12,7 +12,7 @@ process SPLIT_KINGDOMS { conda (params.enable_conda ? "bioconda::autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/modules/local/unclustered_recruitment.nf b/modules/local/unclustered_recruitment.nf index dee238caf..460bf1b9a 100644 --- a/modules/local/unclustered_recruitment.nf +++ b/modules/local/unclustered_recruitment.nf @@ -12,7 +12,7 @@ process RECRUIT { conda (params.enable_conda ? "autometa" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/subworkflows/local/prepare_ncbi_taxinfo.nf b/subworkflows/local/prepare_ncbi_taxinfo.nf index b11c39c7c..3132f15c1 100644 --- a/subworkflows/local/prepare_ncbi_taxinfo.nf +++ b/subworkflows/local/prepare_ncbi_taxinfo.nf @@ -71,7 +71,7 @@ process DOWNLOAD_TAXDUMP { conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } diff --git a/subworkflows/local/prepare_nr.nf b/subworkflows/local/prepare_nr.nf index da70d61cc..0d1de4b68 100644 --- a/subworkflows/local/prepare_nr.nf +++ b/subworkflows/local/prepare_nr.nf @@ -16,7 +16,7 @@ process DOWNLOAD_NR { conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" } @@ -46,7 +46,7 @@ process TEST_DOWNLOAD { conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" + container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0" } else { container "jasonkwan/autometa:${params.autometa_image_tag}" }