build updates

Author: terhorst

.travis.yml

@@ -16,7 +16,7 @@ install:
   - conda install conda-build anaconda-client constructor
   - conda/template.py conda/meta.tpl $VERSION > conda/meta.yaml 
   - conda build -c terhorst -c conda-forge -c bioconda conda
-  - conda install --use-local smcpp
+  - conda install --use-local -c terhorst -c bioconda -c conda-forge smcpp
   - echo `which smc++`
   - test/integration/test.sh `which smc++`
   - conda/template.py conda/construct.tpl $VERSION > conda/construct.yaml 

conda/run_test.sh

@@ -0,0 +1,17 @@
+#!/bin/bash -x
+SMC=smc++
+set -e
+$SMC vcf2smc example/example.vcf.gz /tmp/example.1.smc.gz 1 msp1:msp_0,msp_1
+$SMC vcf2smc example/example.vcf.gz /tmp/example.2.smc.gz 1 msp2:msp_2
+$SMC vcf2smc example/example.vcf.gz /tmp/example.12.smc.gz 1 msp1:msp_0,msp_1 msp2:msp_2
+$SMC estimate -o /tmp/out/1 --theta .00025 --em-iterations 1 /tmp/example.1.smc.gz
+$SMC estimate -o /tmp/out/2 --theta .00025 --em-iterations 1 /tmp/example.2.smc.gz
+$SMC estimate -o /tmp/out/12 --theta .00025 --em-iterations 1 /tmp/example.12.smc.gz
+$SMC split -o /tmp/out/split --em-iterations 1 \
+    /tmp/out/1/model.final.json \
+    /tmp/out/2/model.final.json \
+    /tmp/example.*.smc.gz
+$SMC plot -c -g 29 --logy /tmp/1.png /tmp/out/1/model.final.json
+$SMC plot /tmp/2.pdf /tmp/out/2/model.final.json
+$SMC plot -c --logy /tmp/12.png /tmp/out/12/model.final.json
+$SMC plot -c --logy /tmp/all.pdf /tmp/out/*/model.final.json