Add coding exons packages

Author: mikecormier

Data_managment.png

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+.. _`grch37-coding-exons-ensembl-v1`:
+
+grch37-coding-exons-ensembl-v1
+==============================
+
+|downloads|
+
+Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from Ensembl gene sets. All other features, including non-coding exon features and non-protein coding exon features, have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: exon (exons that overlap coding regions in protein coding genes). Features are in GTF format.
+
+================================== ====================================
+GGD Package                        grch37-coding-exons-ensembl-v1 
+Species                            Homo_sapiens
+Genome Build                       GRCh37
+GGD Channel                        ggd-genomics
+Package Version                    1
+Recipe Author                      mjc 
+Data Provider                      Ensembl
+Data Version                       release-75_2-6-14
+Genomic File Type                  gtf
+Data file coordinate basing        1-based-inclusive
+Package's Data Files               grch37-coding-exons-ensembl-v1.gtf.gz, grch37-coding-exons-ensembl-v1.gtf.gz.tbi
+Approximate Size of Each Data File grch37-coding-exons-ensembl-v1.gtf.gz: **12.20M**, grch37-coding-exons-ensembl-v1.gtf.gz.tbi: **465.25K**
+Package Keywords                   Gene-Features, GTF, Ensembl-GTF, Ensembl-Gene-Set, Annotated-Transcripts, Protein-Coding-Exon-Features, Coding-Exon, Protein-Coding-Exons
+Package Dependencies:              gsort, htslib, zlib
+Recipe                             https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-coding-exons-ensembl-v1
+================================== ====================================
+
+Install with ``--prefix``
+-------------------------
+**Prefix install enabled:** *True*
+
+Installation
+------------
+
+.. highlight: bash
+
+With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
+
+   ggd install -c ggd-genomics grch37-coding-exons-ensembl-v1
+
+.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-coding-exons-ensembl-v1/badges/downloads.svg
+               :target: https://anaconda.org/ggd-genomics/grch37-coding-exons-ensembl-v1

Figure_1.png

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+.. _`grch37-coding-exons-gencode-v1`:
+
+grch37-coding-exons-gencode-v1
+==============================
+
+|downloads|
+
+Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from  the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features, including non-coding exon features and non-protein coding exon features, have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: exon (exons that overlap coding regions in protein coding genes). 
+
+================================== ====================================
+GGD Package                        grch37-coding-exons-gencode-v1 
+Species                            Homo_sapiens
+Genome Build                       GRCh37
+GGD Channel                        ggd-genomics
+Package Version                    1
+Recipe Author                      mjc 
+Data Provider                      GENCODE
+Data Version                       release-34_03-24-2020
+Genomic File Type                  gtf
+Data file coordinate basing        1-based-inclusive
+Package's Data Files               grch37-coding-exons-gencode-v1.gtf.gz, grch37-coding-exons-gencode-v1.gtf.gz.tbi
+Approximate Size of Each Data File grch37-coding-exons-gencode-v1.gtf.gz: **21.10M**, grch37-coding-exons-gencode-v1.gtf.gz.tbi: **474.19K**
+Package Keywords                   Gene-Features, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts, Protein-Coding-Exon-Features, Coding-Exon, Protein-Coding-Exons
+Package Dependencies:              grch37-chrom-mapping-ucsc2ensembl-ncbi-v1, gsort, htslib, zlib
+Recipe                             https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-coding-exons-gencode-v1
+================================== ====================================
+
+Install with ``--prefix``
+-------------------------
+**Prefix install enabled:** *True*
+
+Installation
+------------
+
+.. highlight: bash
+
+With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
+
+   ggd install -c ggd-genomics grch37-coding-exons-gencode-v1
+
+.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-coding-exons-gencode-v1/badges/downloads.svg
+               :target: https://anaconda.org/ggd-genomics/grch37-coding-exons-gencode-v1