Add librg-pp-bundle-perl and profdisis packages

* ppflat2xml and profdisis are now installed in build
* Addresses internal issues #68 and #27

Dockerfile

@@ -13,7 +13,7 @@ RUN mkdir -p /usr/share/man/man1
 # Install public keys for repos
 RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys FCAE2A0E115C3D8A && \
     apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 228FE7B0D6EBED94 && \
-    apt-key adv --keyserver hkp://pool.sks-keyservers.net:80 --recv-keys 0xA5D32F012649A5A9
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0xA5D32F012649A5A9
 
 # So we can get packages from https repos and some necessary utilities
 # By removing /var/lib/apt/lists it reduces the image size, since the apt cache is not stored in a layer.
@@ -54,9 +54,11 @@ RUN dpkg -i /tmp/libboost-system1.49.0_1.49.0-3.2_amd64.deb && \
 RUN apt-get update && \
     apt-get install -y --allow-unauthenticated rostlab-debian-keyring && \
     apt-get install -y \
+    librg-pp-bundle-perl \
     pp-cache-mgr \
     predictprotein \
-    predictprotein-nonfree && \
+    predictprotein-nonfree \
+    profdisis && \
     rm -rf /var/lib/apt/lists/*
 
 # Now that the packages are installed, copy configs and make necessary ones

README.md

@@ -7,13 +7,14 @@ The Docker image this creates is the exact version that runs on our cluster at [
 
 In an effort to preserve the current (as of 2020-09-08) version of predictprotein, including all of the methods it uses, this Dockerfile and its supporting packages, configuration files, and scripts, have been created, which will allow predictprotein to be able to be run from any current and (hopefully) future Docker-supported operating system.
 
-The produced Docker image will also include the suite of `pp-cache-mgr` utilities, which store, fetch, and manage predictprotein results which are stored in a hashed-indexed cache.
+The produced Docker image will also include the suite of `pp-cache-mgr` and `librg-pp-bundle-perl` utilities, which store, fetch, parse, and manage predictprotein results which are stored in a hashed-indexed cache.
 These utilities include:
 * `ppc_configtest` - PredictProtein cache config file sanity check
 * `ppc_fetch`      - fetch results from PredictProtein cache
 * `ppc_hash`       - print PredictProtein result hash
 * `ppc_lock`       - lock a cache slot
 * `ppc_store`      - store results into PredictProtein cache
+* `ppflat2xml`     - converts PredictProtein methods output to xml
 
 Although only the packages and data models necessary for its proper functioning have been installed, the produced Docker image will be larger than 12GB (!) in size, which doesn't include the necessary databases needed.