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--- cluster:73 [2021/06/10 12:55]
hmeij07 [Ovito]
+++ cluster:73 [2021/06/22 19:18]
hmeij07 [Miniconda3]
@@ Line 18: / Line 18: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== VSEARCH ======
+VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization ... an alternative to USEARCH; offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
+  * https://github.com/torognes/vsearch
+  * requires centos7
+  * centos7 queues; mwgpu, amber128, exx96
+    * debug host greentail52
+  * /share/apps/CENTOS7/vsearch/2.17.0/bin/vsearch
+====== DeepChem ======
+ DeepChem is a deep learning tool built for bio/chem research
+  * First installed latest Miniconda
+  * /share/apps/CENTOS7/amber/miniconda3, see below
+    * put the code block below in ~/.bashrc and log back in
+  * https://deepchem.io/
+    * installed stable/conda/gpu=no
+  * pip installed tensorflow-2.5
+  * Note: miniconda contains (Your python: python=3.8)
+    * "conda install -c ambermd pytraj" fails to install
+  * CentOS7 so queues mwgpu, amber128, exx96
+    * or for debugging use greentail52
+<code>
+# add to ~/.bashrc and log back in, then check: 'which python pip conda'
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/share/apps/CENTOS7/amber/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="/share/apps/CENTOS7/amber/miniconda3/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+</code>
+<code>
+Successfully installed absl-py-0.12.0 astunparse-1.6.3
+cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2
+google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1
+h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2
+markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0
+protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0
+rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1
+tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0
+termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
+</code>
+====== Miniconda3 ======
+  * add to ~/.bashrc and log back in, then check: 'which python pip conda'
+    * the code block is list under DeepChem section above
+<code>
+# https://github.com/mtazzari/galario
+conda install -c conda-forge galario
+  fftw               conda-forge/linux-64::fftw-3.3.8-nompi_hfc0cae8_1114
+  galario            conda-forge/linux-64::galario-1.2.2-py38h9d68f60_1002
+  libblas            conda-forge/linux-64::libblas-3.9.0-8_openblas
+  libcblas           conda-forge/linux-64::libcblas-3.9.0-8_openblas
+  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_19
+  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_19
+  liblapack          conda-forge/linux-64::liblapack-3.9.0-8_openblas
+  libopenblas        conda-forge/linux-64::libopenblas-0.3.12-pthreads_hb3c22a3_1
+  numpy              conda-forge/linux-64::numpy-1.19.4-py38hf0fd68c_1
+  python_abi         conda-forge/linux-64::python_abi-3.8-1_cp38
+  scipy              conda-forge/linux-64::scipy-1.5.3-py38h828c644_0
+</code>
 ====== pytraj ======
+ Pytraj is a wrapper for cpptraj
   * https://amber-md.github.io/pytraj/latest/installation.html#installation
@@ Line 28: / Line 111: @@
   * python ./setup.py install
   * requires CentOS7 so queues mwgpu, amber128 and exx96
+  * or for debugging use greentail52
+  * /share/apps/CENTOS7/amber/pytraj
@@ Line 326: / Line 411: @@
   * picked up mpirun from miniconda2 apps (that may be a problem)
-  * Added to 3.8.3 "acpipe"
+  * Added to 3.8.3 "acpype"
   * https://github.com/alanwilter/acpype
+From website:\\
+"
+We now have an up to date webservice at http://bio2byte.be/acpype/ \\
+(but it does not have the amb2gmx funcionality).
+To run acpype, locally, with its all functionalities, you need ANTECHAMBER from package AmberTools and Open Babel if your input files are of PDB format.
+However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing at all but Python.
+"\\
  --- //[[hmeij@wesleyan.edu|Henk]] 2021/02/18 14:41//

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