Initial commit

README.md

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+# artic-base
+A base template for an implementation of an ARTIC install. This can be forked and modified for specific use-cases. To do this, click the green 'Use this template' button above. You can then give your new repository a name.
+
+You can modify the existing files to suit your use-case but avoid moving or renaming any files or directories that are in this template.
+
+If the template is updated, you will be able to merge these changes into your repository as needed.
+
+To install the `Conda` environment use:
+
+```
+conda env create -f environment.yml -n <environment name>
+```
+
+Where `<environment_name>` is the name you want to use (probably the same as the repo).
+
+Then activate the environment using:
+
+```
+conda activate <environment name>
+```

environment.yml

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+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3
+  - nodejs=12
+  - biopython=1.70=np112py36_1
+  - bwa=0.7.17=pl5.22.0_2
+  - clint=0.5.1=py36_0
+  - eigen=3.2=3
+  - pysam=0.11.2.2=py36_1
+  - pyvcf=0.6.8=py36_0
+  - ete3=3.1.1=py36_0
+  - goalign=0.2.8=0
+  - gotree=0.2.10=0
+  - libdeflate=0.8=0
+  - muscle=3.8.1551=2
+  - nanopolish=0.9.2=py36_ncurses5.9_4
+  - phyml=3.3.20190909 # references etetoolkit build
+  - pandas=0.23.0=py36_1
+  - samtools=1.8=4
+  - mafft=7.407=0
+  - iqtree=1.6.12
+  - datrie=0.8
+  - artic-network::rampart=1.0
+  - pip
+  - pip:
+    - git+https://github.com/artic-network/fieldbioinformatics.git
+    - git+https://github.com/artic-network/[email protected]

rampart/README.md

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+# RAMPART
+
+This folder contains example files for running RAMPART. Modify and adapt these to the specific instance being developed.

rampart/primers.json

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+{
+	"name": "EBOV primer scheme v3.0",
+	"amplicons": [
+		[37, 427],
+		[333, 726],
+		[641, 1021],
+		[922, 1322],
+		[1250, 1635],
+		[1542, 1949],
+		[1860, 2253],
+		[2161, 2553],
+		[2383, 2763],
+		[2699, 3085],
+		[2974, 3361],
+		[3296, 3684],
+		[3610, 4010],
+		[3900, 4303],
+		[4239, 4622],
+		[4565, 4948],
+		[4867, 5274],
+		[5182, 5562],
+		[5474, 5880],
+		[5791, 6189],
+		[6121, 6512],
+		[6439, 6820],
+		[6738, 7142],
+		[7079, 7460],
+		[7377, 7773],
+		[7698, 8096],
+		[8003, 8388],
+		[8330, 8711],
+		[8618, 9035],
+		[8947, 9359],
+		[9267, 9685],
+		[9603, 9992],
+		[9895, 10279],
+		[10176, 10563],
+		[10487, 10869],
+		[10788, 11169],
+		[11048, 11431],
+		[11298, 11711],
+		[11646, 12027],
+		[11939, 12341],
+		[12234, 12637],
+		[12546, 12941],
+		[12843, 13232],
+		[13161, 13541],
+		[13443, 13860],
+		[13778, 14171],
+		[14097, 14477],
+		[14395, 14803],
+		[14675, 15061],
+		[14994, 15374],
+		[15281, 15661],
+		[15602, 15986],
+		[15899, 16297],
+		[16206, 16591],
+		[16505, 16911],
+		[16849, 17230],
+		[17145, 17551],
+		[17445, 17861],
+		[17800, 18183],
+		[18082, 18474],
+		[18404, 18788],
+		[18542, 18922]
+	]
+}

rampart/protocol.json

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+{
+  "name": "ARTIC Ebola virus protocol v2.0",
+  "description": "Amplicon based sequencing of Ebola virus (Zaire species).",
+  "url": "http://artic.network/"
+}