Release 5
Release 5
February 12, 2020
Activated
Description
Optimized asap_run docker, migration of v.2.7 python scripts to v.3.0. Updated Ensembl data in asap_data database.
Compliance Schemas
sc
scFAIR v7.1.0
(scFAIR schema v7.1.0)
Schema reference
Website
Loom Path Translation
Required for publishing
scFAIR validates single-cell transcriptomics datasets against the scFAIR cell metadata schema
Badges:
Tool Versions
| Tool | Version |
|---|---|
| java_stats | 1.0 |
| h5py | 2.10.0 |
| scikits_learn | 0.22.1 |
| numpy | 1.18.1 |
| scipy | 1.4.1 |
| java | 11.0.6 |
| python | 3.7.6 |
| stats | 3.6.0 |
| sc3 | 1.14.0 |
| cluster | 2.1.0 |
| rtsne | 0.15 |
| limma_voom | 3.42.2 |
| deseq2 | 1.26.0 |
| umap-learn | 0.3.10 |
| datatable | 1.12.8 |
| go_db | 2020-Jan |
| ensembl_vertebrate | 101 |
| ensembl_genomes | 58 |
Docker Images
Raw metadata
{
"name": "fabdavid/asap_run",
"tag": "v5",
"version": 5,
"call": "docker run #host_option --name #container_name --network=asap2_asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap2:/data/asap2 -v /srv/asap_run/srv:/srv #image_name -c"
}
DockerImage.tools_json
{
"r": "3.6.2",
"hdf5r": "1.3.4",
"scran": "1.14.6",
"xvector": "0.26.0",
"sc3": "1.14.0",
"scater": "1.14.6",
"cluster": "2.1.0",
"limma_voom": "3.42.2",
"deseq2": "1.26.0",
"combat": "3.34.0",
"genefilter": "1.68.0",
"m3drop": "3.10.4",
"rhdf5": "2.31.11",
"seurat": "3.1.5",
"future.apply": "1.5.0",
"plotly": "4.9.2.1",
"statmod": "1.4.34",
"devtools": "2.3.0",
"datatable": "1.12.8",
"jsonlite": "1.6.1",
"rtsne": "0.15",
"r6": "2.4.1",
"sanon": "1.6",
"reticulate": "1.15",
"edger": "3.28.1",
"python3": "3.7.6",
"h5py": "3.1.0",
"leidenalg": "0.8.7",
"loompy": "3.0.6",
"louvain": "0.7.0",
"matplotlib": "3.3.2",
"numba": "0.53.1",
"numpy": "1.20.3",
"pandas": "1.2.4",
"scikit_learn": "0.24.2",
"scipy": "1.6.3",
"umap_learn": "0.5.1",
"java": "11.0.6"
}
fabdavid/asap_run (v5)
Java
Python
R
Raw environment JSON
{"tool_versions":{"java_stats":"1.0","h5py":"2.10.0","scikits_learn":"0.22.1","numpy":"1.18.1","scipy":"1.4.1","java":"11.0.6","python":"3.7.6","stats":"3.6.0","sc3":"1.14.0","cluster":"2.1.0","rtsne":"0.15","limma_voom":"3.42.2","deseq2":"1.26.0","umap-learn":"0.3.10","datatable":"1.12.8","go_db":"2020-Jan","ensembl_vertebrate":"101","ensembl_genomes":"58"},"asap_data_db_version":5,"docker_images":{"asap_run":{"name":"fabdavid/asap_run","tag":"v5","version":5,"call":"docker run #host_option --name #container_name --network=asap2_asap_network -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v /data/asap2:/data/asap2 -v /srv/asap_run/srv:/srv #image_name -c"}},"time_call":"time -o '#output_dir/exec_run_details.log' -f 'U=%U,S=%S,E=%E,P=%P,X=%X,D=%D,M=%M,K=%K,t=%t,I=%I,O=%O,F=%F,R=%R,W=%W' ","exec_stdout":"#output_dir/exec.out","exec_stderr":"#output_dir/exec.err","hosts":{"localhost":{"nb_cores":80}},"asap_run_java":"ASAP-2.0.jar","types":{"dataset":{"description":"Matrix of values of any dimension and containing any type of data"},"int_matrix":{"description":"Count matrix (the matrix must contain only integer values)"},"num_matrix":{"description":"Numeric matrix (the matrix can contain integer or floating point values)"},"with_mdata_ercc":{"description":"Metadata for ERCC must exist."},"discrete_mdata":{"description":"Categorical metadata"},"numeric_mdata":{"description":"Numerical metadata"},"string_mdata":{"description":"Text metadata"},"col_mdata":{"description":"Cell metadata"},"row_mdata":{"description":"Gene metadata"},"mdata":{"description":"Metadata"}},"dashboards":{"std_runs":{"icon_class":"fa fa-bars"},"dim_reduction":{"icon_class":"scatter_plot-icon"}},"compliance":{"1":[{"name":"scFAIR","version":"7.1.0","source_schema_name":"scFAIR schema","description":"scFAIR validates single-cell transcriptomics datasets against the scFAIR cell metadata schema","source_url":"https://github.com/scFAIR/scFAIR/blob/main/schema/7.1.0/README.md","url":"https://sc-fair.org","compliant_icon":"scfair_badge_compliant.svg","not_compliant_icon":"scfair_badge_noncompliant.svg","if_compliant":["allow_public"]}]},"asap_data_db_name":"asap_data_v5"}