update shell script

uc-cdis · Jan 17, 2021 · 2c1a636 · 2c1a636
1 parent 40428a8
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Showing 4 changed files with 50 additions and 2 deletions.
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ copy credentials.json gen3-augur/config
 ## Using Conda
 An `environment.yml` file is provided and can be used to build a virtual environment containing all dependencies. Create the environment using:
 ```
-conda env create -f enviroment.yml
+conda env create -f environment.yml
 ```
 Then activate the environment for use:
 ```

diff --git a/config/credentials.json b/config/credentials.json
@@ -0,0 +1,4 @@
+{
+	"api_key": "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV8yMDIwLTAzLTE4VDE4OjIwOjI3WiJ9.eyJwdXIiOiJhcGlfa2V5IiwiYXVkIjpbImRhdGEiLCJ1c2VyIiwiZmVuY2UiLCJvcGVuaWQiXSwic3ViIjoiMjkiLCJpc3MiOiJodHRwczovL2NoaWNhZ29sYW5kLnBhbmRlbWljcmVzcG9uc2Vjb21tb25zLm9yZy91c2VyIiwiaWF0IjoxNjEwOTIyNzY0LCJleHAiOjE2MTM1MTQ3NjQsImp0aSI6ImU5YzZmZTU3LTNlZjUtNDNhZi04MjRiLWM4MTc3ODhjMjdiYyIsImF6cCI6IiJ9.TFJ11LtZ4RRM6WTnO4k1P1z0cPrm-nEI0eE1sr6F45VFY9g4ohFcEASJEzUOzdmIqsF0JlHj9RhPvvRlxejxhZSS1Zd9OWvCvZfUE5DRFqWR8hCAbto00Th0H3qf_mwXNI6rw2oDCJ-YgH13KX0xQA7ANgaa99LQX_B0fTaTZTijZd1YAPxSAQXJwp4uhlMsR94ldDao4YDVJSPU5kae96QvMY5kNxeOkSmFR65DCky7RiPXvZx2K4vyPDdZ89oir81wWBedtZ7wW3g8GFcUdNsUsXY8OLbPM8XOicdk6e-i4KRCgfrk2nU5BiqyE8-A78op_LUGUygytq_U8dPI9Q",
+	"key_id": "e9c6fe57-3ef5-43af-824b-c817788c27bc"
+}
diff --git a/gen3-augur-fasta.sh b/gen3-augur-fasta.sh
@@ -0,0 +1,41 @@
+#!/bin/sh
+set -ex
+
+today=$(date +'%m%d%y')
+
+# Run Augur pipeline
+# Filter
+echo "Filter fasta files"
+augur filter --sequences data/covid19_Gagnon_Chicago_${today}.fasta --metadata data/covid19_Gagnon_Chicago_${today}.csv --output results/covid19_${today}_filter.fasta &&
+
+# Alignment(default mafft tool)
+echo "Run alignment"
+augur align --sequences results/covid19_${today}_filter.fasta --reference-sequence config/sequence.gb --output results/covid19_${today}_aligned.fasta --fill-gaps --nthreads auto &&
+
+# Create raw tree
+echo "Create raw tree"
+augur tree --alignment results/covid19_${today}_aligned.fasta --output results/covid19_${today}_tree_raw.nwk --nthreads auto &&
+
+# Refine tree
+echo "Refine tree"
+augur refine --tree results/covid19_${today}_tree_raw.nwk --alignment results/covid19_${today}_aligned.fasta --metadata data/covid19_Gagnon_Chicago_${today}.csv --output-tree results/covid19_${today}_tree.nwk --output-node-data results/covid19_${today}_branch_lengths.json --timetree --coalescent opt --date-confidence --date-inference marginal --clock-filter-iqd 4 &&
+
+# Refine traits
+echo "Refine traits"
+augur traits --tree results/covid19_${today}_tree.nwk --metadata data/covid19_Gagnon_Chicago_${today}.csv --output results/covid19_${today}_traits.json --columns location --confidence &&
+
+# Ancestry Inference
+echo "Infer ancestry"
+augur ancestral --tree results/covid19_${today}_tree.nwk --alignment results/covid19_${today}_aligned.fasta --output-node-data results/covid19_${today}_nt_muts.json --inference joint &&
+
+# Mutation Translate
+echo "Mutation translation"
+augur translate --tree results/covid19_${today}_tree.nwk --ancestral-sequences results/covid19_${today}_nt_muts.json --reference-sequence config/sequence.gb --output results/covid19_${today}_aa_muts.json &&
+
+# Labeling clades as specified in config/clades.tsv
+augur clades --tree results/covid19_${today}_tree.nwk --mutations results/covid19_${today}_nt_muts.json results/covid19_${today}_aa_muts.json --clades config/clades.tsv --output results/covid19_${today}_clade.json
+
+
+# Export json
+echo "Export json"
+augur export v2 --tree results/covid19_${today}_tree.nwk --metadata data/covid19_Gagnon_Chicago_${today}.csv --node-data results/covid19_${today}_branch_lengths.json results/covid19_${today}_traits.json results/covid19_${today}_nt_muts.json results/covid19_${today}_aa_muts.json results/covid19_${today}_clade.json --colors config/color_schemes.tsv --lat-longs config/latitude_longitude.tsv --auspice-config config/auspice_config.json --output auspice/covid19_${today}.json
diff --git a/gen3-augur.sh b/gen3-augur.sh
@@ -57,6 +57,9 @@ augur ancestral --tree results/covid19_${today}_tree.nwk --alignment results/cov
 echo "Mutation translation"
 augur translate --tree results/covid19_${today}_tree.nwk --ancestral-sequences results/covid19_${today}_nt_muts.json --reference-sequence config/sequence.gb --output results/covid19_${today}_aa_muts.json &&
 
+# Labeling clades as specified in config/clades.tsv
+augur clades --tree results/covid19_${today}_tree.nwk --mutations results/covid19_${today}_nt_muts.json results/covid19_${today}_aa_muts.json --clades config/clades.tsv --output results/covid19_${today}_clade.json
+
 # Export json
 echo "Export json"
-augur export v2 --tree results/covid19_${today}_tree.nwk --metadata data/covid19_${today}_genbank.csv --node-data results/covid19_${today}_branch_lengths.json results/covid19_${today}_traits.json results/covid19_${today}_nt_muts.json results/covid19_${today}_aa_muts.json --colors config/color_schemes.tsv --lat-longs config/latitude_longitude.tsv --auspice-config config/auspice_config.json --output auspice/covid19_${today}.json
+augur export v2 --tree results/covid19_${today}_tree.nwk --metadata data/covid19_${today}_genbank.csv --node-data results/covid19_${today}_branch_lengths.json results/covid19_${today}_traits.json results/covid19_${today}_nt_muts.json results/covid19_${today}_aa_muts.json results/covid19_${today}_clade.json --colors config/color_schemes.tsv --lat-longs config/latitude_longitude.tsv --auspice-config config/auspice_config.json --output auspice/covid19_${today}.json