From 09182a0a69b8952947bf797e677302f1d82d8fc2 Mon Sep 17 00:00:00 2001
From: AndrewCRMartin <andrew@bioinf.org.uk>
Date: Tue, 24 Oct 2017 13:29:52 +0100
Subject: [PATCH] Updates to install docs and script

---
 .gitignore                                    | 10 +++--
 ...dLine.txt => 00INSTALL_CommandLineOnly.txt |  0
 00INSTALL_WebInterface.md                     | 40 +++++++++++++++++++
 install.sh                                    | 10 ++---
 web/config_home.cfg                           |  3 +-
 web/config_ucl.cfg                            |  3 +-
 web/index.tt                                  | 11 ++++-
 7 files changed, 66 insertions(+), 11 deletions(-)
 rename 00INSTALL_CommandLine.txt => 00INSTALL_CommandLineOnly.txt (100%)
 create mode 100644 00INSTALL_WebInterface.md

diff --git a/.gitignore b/.gitignore
index c17f31a..8175fd6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,10 @@ data/consScores/FOSTA/*
 data/consScores/BLAST/*
 data/IntPred/*.model*
 setup.sh
-packages/bioptools-1.4.tar.gz
-packages/bioptools-1.4/
-packages/TCNlib-0.1/
\ No newline at end of file
+packages/bioptools-*.tar.gz
+web/footer.tt
+web/header.tt
+web/menu.tt
+web/Makefile
+web/config.cfg
+web/index.html
diff --git a/00INSTALL_CommandLine.txt b/00INSTALL_CommandLineOnly.txt
similarity index 100%
rename from 00INSTALL_CommandLine.txt
rename to 00INSTALL_CommandLineOnly.txt
diff --git a/00INSTALL_WebInterface.md b/00INSTALL_WebInterface.md
new file mode 100644
index 0000000..5372baf
--- /dev/null
+++ b/00INSTALL_WebInterface.md
@@ -0,0 +1,40 @@
+IntPred Web Server Install
+==========================
+
+1. Create a directory in your web hierarchy - e.g.
+```/home/httpd/html/intpred2```
+
+2. Clone the IntPred repository into a directory. This will be where
+IntPred is installed. It doesn't have to be in the web hierarchy, but
+I suggest that it is. e.g.
+```
+cd /home/httpd/html/intpred2/
+git clone git@github.com:ACRMGroup/IntPred.git
+```
+
+3. Install IntPred from the cloned directory. e.g.
+```
+cd /home/httpd/html/intpred2/IntPred
+./install.sh
+source ./setup.sh
+```
+You must be root or have sudo permissions to do this. See the notes in
+`00INSTALL_CommandLine.txt` (`README.md`) for more details.
+
+4. Change to the `web` sub-directory of IntPred to your web
+Create/modify the config.cfg file as required
+```
+cd /home/httpd/html/intpred2/IntPred/web
+emacs config.cfg
+```
+
+5. Run the configure script, build and install the web pages:
+```
+./configure.pl
+make
+make install
+```
+See notes in the `web/README.md` file on Apache configuration.
+
+
+
diff --git a/install.sh b/install.sh
index 70ec67c..8798613 100755
--- a/install.sh
+++ b/install.sh
@@ -55,7 +55,7 @@ o conf commit
 EOF
 fi
 
-if promptUser "Install Perl dependencies including BioPerl?"; then
+if promptUser "Install Perl dependencies including BioPerl (for the Perl you are using)?"; then
     yes | sudo $PERL -MCPAN -e shell <<EOF
 force install CPAN::Meta::Requirements
 force install Math::VectorReal
@@ -92,12 +92,12 @@ EOF
     yes | sudo $PERL ./installScripts/installBioperl.pl -perl=$PERL
 fi
 
-if promptUser "Download and install the IntPred model file?"; then
+if promptUser "Download and install the IntPred model file? (Required for a new install)"; then
     # Download the WEKA model file
     ./installScripts/getIntPredModel.sh
 fi
 
-if promptUser "Install TCNlib and dependencies?"; then
+if promptUser "Install TCNlib and dependencies? (Required for a new install)"; then
    # TCNlib
     cd $H/packages
     tar xvf TCNlib-${TCNLIBVERSION}.tar.gz
@@ -106,11 +106,11 @@ if promptUser "Install TCNlib and dependencies?"; then
     cd $H/packages/TCNlib-${TCNLIBVERSION}
     $PERL ./setup.pl -perl=$PERL
 
-    if promptUser "Download and install BLAST database?"; then
+    if promptUser "Download and install BLAST database? (Required for a new install)"; then
         ./setup-blastdb -f
     fi
 
-    if promptUser "Install BiopTools?"; then
+    if promptUser "Install BiopTools? (Required for a new install)"; then
         cd $H/packages
         wget $BIOPTOOLSURL
         mv V${BIOPTOOLSVERSION}.tar.gz bioptools-${BIOPTOOLSVERSION}.tar.gz
diff --git a/web/config_home.cfg b/web/config_home.cfg
index cd2d876..97c07bb 100644
--- a/web/config_home.cfg
+++ b/web/config_home.cfg
@@ -6,9 +6,10 @@ ipbin=${iphome}/bin
 pdbdir=/nas/backup/work/newserver/data/pdb
 pdbprep=pdb
 pdbext=.ent
+tcnlibversion=0.1.1
 
 # these are just used during the install
 menu=`pwd`/menu_default.tt
 header=`pwd`/header_default.tt
 footer=`pwd`/footer_default.tt
-pdbcache=`pwd`/../packages/TCNlib-0.1/data/pdb-cache
+pdbcache=`pwd`/../packages/TCNlib-${tcnlibversion}/data/pdb-cache
diff --git a/web/config_ucl.cfg b/web/config_ucl.cfg
index 40e236a..615642e 100644
--- a/web/config_ucl.cfg
+++ b/web/config_ucl.cfg
@@ -6,9 +6,10 @@ ipbin=${iphome}/bin
 pdbdir=/acrm/data/pdb
 pdbprep=pdb
 pdbext=.ent
+tcnlibversion=0.1.1
 
 # these are just used during the install
 menu=`pwd`/menu_default.tt
 header=`pwd`/header_default.tt
 footer=`pwd`/footer_default.tt
-pdbcache=`pwd`/../packages/TCNlib-0.1/data/pdb-cache
+pdbcache=`pwd`/../packages/TCNlib-${tcnlibversion}/data/pdb-cache
diff --git a/web/index.tt b/web/index.tt
index da25a99..2b520d7 100644
--- a/web/index.tt
+++ b/web/index.tt
@@ -19,8 +19,17 @@
         and specificity at the expense of
         sensivity. [<a href='paper/intpred.pdf'>Paper as
           submitted</a>][<a href='paper/SupplementaryMaterial.pdf'>Supplementary
-          Material</a>]
+          Material</a>][<a href='paper/Datasets.xls'>Datasets</a>]
       </p>
+
+<!-- Status Messages -->
+<!--
+      <div class='alert alert-info'>
+        24.10.17 Apologies! The server had stopped working owing to a change in
+        where files are stored at the RCSB PDB site. This is now fixed.
+      </div>
+-->
+
     </div>
   </div>