From 18c972b59d7c423c31d81bd699b9f1568ce79de8 Mon Sep 17 00:00:00 2001
From: Tru Huynh <tru@pasteur.fr>
Date: Thu, 13 Jul 2017 20:32:26 +0200
Subject: [PATCH] IMP tutorial + IMP(dev, not released version)
---
ISB2017/installation_notes/imp-dev.md | 41 ++++++++++++++++++++++
ISB2017/installation_notes/imp-tutorial.md | 19 ++++++++++
ISB2017/installation_notes/imp.md | 3 +-
ISB2017/modulefiles/IMP | 13 ++++---
4 files changed, 70 insertions(+), 6 deletions(-)
create mode 100644 ISB2017/installation_notes/imp-dev.md
create mode 100644 ISB2017/installation_notes/imp-tutorial.md
diff --git a/ISB2017/installation_notes/imp-dev.md b/ISB2017/installation_notes/imp-dev.md
new file mode 100644
index 0000000..de4125a
--- /dev/null
+++ b/ISB2017/installation_notes/imp-dev.md
@@ -0,0 +1,41 @@
+# IMP (development version)
+- reuse anaconda2 setup
+```
+module purge
+module add anaconda2
+git clone https://github.com/salilab/imp
+mkdir imp-build
+cd imp-build
+cmake ../imp -DCMAKE_BUILD_TYPE=Release -DIMP_MAX_LOG=SILENT \
+-DIMP_MAX_CHECKS=NONE \
+-DCMAKE_INCLUDE_PATH=/ISB2017/anaconda2/include/ \
+-DCMAKE_LIBRARY_PATH=/ISB2017/anaconda2/lib \
+-DHDF5_INCLUDE_DIR=/ISB2017/anaconda2/include \
+-DCMAKE_INSTALL_PREFIX=/ISB2017/IMP
+make -j 4 && make install
+cp ~/imp/modules/pmi/pyext/src/process_output.py /ISB2017/IMP/bin/
+```
+
+add the IMP modulefile
+```
+#%Module1.0#####################################################################
+##
+## IMP-co-anaconda2 modulefile
+##
+proc ModulesHelp { } {
+ global dotversion
+
+ puts stderr "\tAdds `/ISB2017/IMP/bin' to your PATH environment variable"
+}
+
+module-whatis "adds `/ISB2017/IMP/bin' to your PATH environment variable"
+
+prepend-path PATH /ISB2017/IMP/bin
+prepend-path PYTHONPATH /ISB2017/IMP/lib64/python2.7/site-packages/
+prepend-path LD_LIBRARY_PATH /ISB2017/IMP/lib64
+module add anaconda2
+# added for Riccardo practical
+module add chimera-1.11.2-linux_x86_64
+module add grace-5.1.25
+```
+
diff --git a/ISB2017/installation_notes/imp-tutorial.md b/ISB2017/installation_notes/imp-tutorial.md
new file mode 100644
index 0000000..09a4cc1
--- /dev/null
+++ b/ISB2017/installation_notes/imp-tutorial.md
@@ -0,0 +1,19 @@
+# IMP tutorial (developper version)
+
+
+# preparing the tarball (for Riccardo)
+```
+git clone https://github.com/salilab/IMP_tutorial
+cd IMP_tutorial/
+git fetch
+git checkout develop
+cd ..
+tar czvf /ISB2017/Course_material/July22/IMP_tutorial.tgz IMP_tutorial/
+```
+
+# usage (for the students)
+```
+cd && tar xzf /ISB2017/Course_material/July22/IMP_tutorial.tgz
+module add IMP
+cd IMP_tutorial/doc && jupyter notebook
+```
diff --git a/ISB2017/installation_notes/imp.md b/ISB2017/installation_notes/imp.md
index f29bd62..bc92a7d 100644
--- a/ISB2017/installation_notes/imp.md
+++ b/ISB2017/installation_notes/imp.md
@@ -1,5 +1,6 @@
# IMP from https://integrativemodeling.org
-- using a separate conda installation tree to avoid conflict from the main anaconda2 tree
+- using a separate conda installation tree to avoid conflict from the main anaconda2 tree
+- stable IMP release (not used from ISB2017)
- https://integrativemodeling.org/download-anaconda.html
```
diff --git a/ISB2017/modulefiles/IMP b/ISB2017/modulefiles/IMP
index c574a9f..3f66bb6 100644
--- a/ISB2017/modulefiles/IMP
+++ b/ISB2017/modulefiles/IMP
@@ -5,11 +5,14 @@
proc ModulesHelp { } {
global dotversion
- puts stderr "\tAdds `/ISB2017/IMP-co-anaconda2/bin' to your PATH environment variable"
+ puts stderr "\tAdds `/ISB2017/IMP/bin' to your PATH environment variable"
}
-module-whatis "adds `/ISB2017/IMP-co-anaconda2/bin' to your PATH environment variable"
+module-whatis "adds `/ISB2017/IMP/bin' to your PATH environment variable"
-prepend-path PATH /ISB2017/IMP-co-anaconda2/bin
-conflict anaconda3
-conflict anaconda2
+prepend-path PATH /ISB2017/IMP/bin
+prepend-path PYTHONPATH /ISB2017/IMP/lib64/python2.7/site-packages/
+prepend-path LD_LIBRARY_PATH /ISB2017/IMP/lib64
+module add anaconda2
+module add chimera-1.11.2-linux_x86_64
+module add grace-5.1.25
--
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