Mercurial > repos > charles-bernard > data_manager_build_alfa_indexes
changeset 6:54c2c66e45a9 draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Thu, 27 Oct 2016 09:17:41 -0400 |
| parents | 6cfa38b014c1 |
| children | 4d8c94b9a6d7 |
| files | data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml data_manager_build_alfa_indexes/tool-data/alfa_indexes.loc.sample~ data_manager_build_alfa_indexes/tool_dependencies.xml |
| diffstat | 4 files changed, 19 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py Thu Oct 27 06:55:32 2016 -0400 +++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py Thu Oct 27 09:17:41 2016 -0400 @@ -231,6 +231,7 @@ logging.info("*** Intial dictionary") logging.info("%s" % params) + shutil.copyfile(stranded_index_name, os.path.join(target_directory, stranded_index_name)) shutil.copyfile(unstranded_index_name, os.path.join(target_directory, unstranded_index_name)) shutil.copyfile(log_file_name, os.path.join(target_directory, log_file_name))
--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml Thu Oct 27 06:55:32 2016 -0400 +++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml Thu Oct 27 09:17:41 2016 -0400 @@ -1,6 +1,12 @@ <tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data"> <description>build ALFA indexes from automatically downloaded gtf annotation file</description> - + <!-- ALFA requires bedtools suite v2.20.0 and above --> + <requirements> + <requirement type="package" version="2.24">bedtools</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.4">matplotlib</requirement> + </requirements> + <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__root_dir__ $__tool_directory__</command> <inputs>
--- a/data_manager_build_alfa_indexes/tool-data/alfa_indexes.loc.sample~ Thu Oct 27 06:55:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#<species> <version> <release> <value> <dbkey> <name> <prefix> -#Arabidopsis_thaliana TAIR10 30 Arabidopsis_t_TAIR10_30 Arabidopsis_t_TAIR10_30 Arabidopsis thaliana: TAIR10 <path_to_alfa_indexes>/Arabidopsis_thaliana.TAIR10.30 -#Drosophila_melanogaster dm6 30 Drosophila_m_dm6_30 Drosophila_m_dm6_30 Drosophila melanogaster: dm6 <path_to_alfa_indexes>/Drosophila_melanogaster.BDGP6.30 -#Homo_sapiens v38 82 Homo_s_v38_82 Homo_s_v38_82 Homo sapiens: v38 <path_to_alfa_indexes>/Homo_sapiens.GRCh38.82 -#Mus_musculus v38 83 Mus_m_v38_83 Mus_m_v38_83 Mus musculus: v38 <path_to_alfa_indexes>/Mus_musculus.GRCm38.83.chr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_alfa_indexes/tool_dependencies.xml Thu Oct 27 09:17:41 2016 -0400 @@ -0,0 +1,11 @@ +<tool_dependency> + <package name="bedtools" version="2.24"> + <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="matplotlib" version="1.4"> + <repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> \ No newline at end of file