MG-RAST · teharrison · Jun 26, 2015 · Feb 6, 2015 · Feb 9, 2015 · Feb 9, 2015
diff --git a/bin/download_m5nr_blast.sh b/bin/download_m5nr_blast.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# set a default values
+# m5nr blast files - 2.6 GB & 11.7 GB
+M5NR_VERSIONS="20100309 20131215"
+TARGET="/m5nr"
+
+for i in $M5NR_VERSIONS; do
+    M5NR_VERSION=$i
+    VERSION_DIR=$TARGET/$M5NR_VERSION
+    URL=ftp://ftp.metagenomics.anl.gov/data/MD5nr/${M5NR_VERSION}/md5nr.blast.tgz
+
+    echo ""
+    echo "TARGET = $TARGET"
+    echo "M5NR_VERSION = $M5NR_VERSION"
+    echo "URL = $URL"
+    echo ""
+
+    if [ -d ${VERSION_DIR} ]; then
+        echo "Files already exist, not downloading"
+    else
+        echo "Downloading files"
+        mkdir -p ${VERSION_DIR}
+        curl -s "${URL}" | tar -zxvf - -C ${VERSION_DIR}
+    fi
+done
+exit 0
diff --git a/bin/fastacmd b/bin/fastacmd
diff --git a/conf/README.md b/conf/README.md
@@ -0,0 +1,27 @@
+
+
+API server
+----------
+
+
+Build image:
+```bash
+export TAG=`date +"%Y%m%d.%H%M"`
+docker build --force-rm --no-cache --rm -t  mgrast/api:${TAG}  https://raw.githubusercontent.com/MG-RAST/MG-RAST/api/docker/Dockerfile
+```
+
+Get config: (private mcs git repo, for details see fleet unit)
+```bash
+if cd /home/core/mgrast-config; then git pull; else cd /home/core/ ; git clone [email protected]:mgrast-config.git ; fi
+```
+
+Download data
+```bash
+docker run -t -i --name api -v /media/ephemeral/api-server-data:/m5nr mgrast/api:${TAG} /MG-RAST/bin/download_m5nr_blast.sh
+docker rm api
+```
+
+Start container:
+```bash
+docker run -t -i --name api -v /home/core/mgrast-config/services/api-server/.postgresql/:/root/.postgresql/:ro -v /home/core/mgrast-config/services/api-server:/api-server-conf -v /media/ephemeral/api-server-data:/m5nr -p 80:80 mgrast/api:${TAG} /usr/local/apache2/bin/httpd -DFOREGROUND -f /MG-RAST/conf/httpd.conf
+```