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comparison readme.rst @ 8:ce135864629c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:27:53 -0400
parents 7adfd0589f49
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7:7adfd0589f49 8:ce135864629c
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12 java -jar snpEff.jar databases | tail -n +3 | cut -f 1,2 | awk '{ gsub(/_/, " ", $2); printf "%s\\t%s : %s\\n", $1, $2, $1 }' | sort -k 2 > snpeffect_genomedb.loc 12 java -jar snpEff.jar databases | tail -n +3 | cut -f 1,2 | awk '{ gsub(/_/, " ", $2); printf "%s\\t%s : %s\\n", $1, $2, $1 }' | sort -k 2 > snpeffect_genomedb.loc
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14 There are 2 datamanagers to download and install prebuilt SnpEff genome databases: 14 There are 2 datamanagers to download and install prebuilt SnpEff genome databases:
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16 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file 16 * data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeffv_databases.loc`` file
17 * data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc`` 17 * data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeffv_databases.loc`` and adds entries to ``snpeffv_genomedb.loc`` and ``snpeffv_regulationdb.loc`` .
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19 SnpEff citation: |Cingolani2012program|_. 19 SnpEff citation: |Cingolani2012program|_.
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21 .. |Cingolani2012program| replace:: Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of *Drosophila melanogaster* strain w1118; iso-2; iso-3. *Fly* 6(2):80-92 21 .. |Cingolani2012program| replace:: Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of *Drosophila melanogaster* strain w1118; iso-2; iso-3. *Fly* 6(2):80-92
22 .. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/ 22 .. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/