Merge pull request #46 from ncbi/release-0.3.0-alpha

Release 0.3.0-alpha

Author: pstrope

PRIVACY.md

@@ -3,4 +3,4 @@
 ## Privacy Statement
 We do not currently collect EGAPx usage data. 
 
-Additional privacy and security policy information can be found on the [NLM Web Policies](https://www.nlm.nih.gov/web_policies.html) page.
+Additional privacy and security policy information can be found on the [NLM Web Policies](https://www.nlm.nih.gov/web_policies.html) page.

README.md

@@ -1,3 +1,6 @@
-genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029//603/195/GCF_029603195.1_ASM2960319v2/GCF_029603195.1_ASM2960319v2_genomic.fna.gz
+genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/029/603/195/GCA_029603195.2_ASM2960319v2/GCA_029603195.2_ASM2960319v2_genomic.fna.gz
 reads: txid2530218[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]
-taxid: 2530218
+taxid: 2530218
+annotation_provider: GenBank submitter
+annotation_name_prefix: GCA_029603195.2
+locus_tag_prefix: egapxtmp

examples/input_C_longicornis.yaml

@@ -1,7 +1,10 @@
-genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
+genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/809/275/GCA_020809275.1_ASM2080927v1/GCA_020809275.1_ASM2080927v1_genomic.fna.gz
 taxid: 6954
 reads:
   - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1
   - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2
   - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1
   - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2
+annotation_provider: GenBank submitter
+annotation_name_prefix: GCA_020809275.1
+locus_tag_prefix: egapxtmp

examples/input_D_farinae_minimal.yaml

@@ -0,0 +1,6 @@
+genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/809/275/GCA_020809275.1_ASM2080927v1/GCA_020809275.1_ASM2080927v1_genomic.fna.gz
+taxid: 6954
+reads: path/to/input_D_farinae_small_reads.txt
+annotation_provider: GenBank submitter
+annotation_name_prefix: GCA_020809275.1
+locus_tag_prefix: egapxtmp

examples/input_D_farinae_small.yaml

@@ -0,0 +1,4 @@
+set1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1
+set1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2
+set2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1
+set2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2