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--- cluster:215 [2025/09/11 14:22] – [Mathematica] hmeij07
+++ cluster:215 [2025/12/10 15:07] (current) – [Structure] hmeij07
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== Miniconda3-py313 =====
+  * https://library.qiime2.org/quickstart/amplicon#id-1-installing-miniconda
+  * module load miniconda3/py313
+    * loads conda modules and ncbi-blast
+  * (cummingsgroup)
+**QIIME**
+<code>
+ source /share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/activate
+ conda init --all
+#
+# To activate this environment, use
+#
+#     $ conda activate qiime2-amplicon-2025.7
+#
+# To deactivate an active environment, use
+#
+#     $ conda deactivate
+base) [hmeij@petaltail ~]$ conda deactivate
+qiime info[hmeij@petaltail ~]$ conda activate qiime2-amplicon-2025.7
+(qiime2-amplicon-2025.7) [hmeij@petaltail ~]$ qiime info
+System versions
+Python version: 3.10.14
+QIIME 2 release: 2025.7
+QIIME 2 version: 2025.7.0
+q2cli version: 2025.7.0
+Installed plugins
+<snip>
+</code>
+**CRABS**
+  * https://github.com/gjeunen/reference_database_creator
+  * /share/apps/CENTOS8/ohpc/software/CRABS/1.0.0/reference_database_creator/crabs
+  * using python from miniconda3-py313
+<code>
+(base) [hmeij@petaltail 1.0.0]$ which python
+/share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/python
+(base) [hmeij@petaltail 1.0.0]$ which pip
+/share/apps/CENTOS8/ohpc/software/miniconda3/py313/bin/pip
+(base)
+# 1-5 python modules installed
+# ncbi-blast downloaded from https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
+export PATH=/share/apps/CENTOS8/ohpc/software/ncbi-blast/2.17.0+/bin:$PATH
+# all 6-10 other packages installed via pip or conda
+# brew install vsearch is a mac command, x86_64 binary not glibc compatible
+# success with conda install vsearch
+</code>
 ===== ChimeraX =====
@@ Line 98: / Line 162: @@
 </code>
+===== Quantum Espresso =====
+  * module q-e/7.3
+  * Description:  Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
+  * URL https://www.quantum-espresso.org/
+  * /share/apps/CENTOS8/ohpc/software/q-e/7.3/bin
+  * openmp and openmpi enabled, no cuda
 ===== Structure =====
@@ Line 377: / Line 449: @@
 </code>
-  * **g_mmpba**
+  * **g_mmpba and gmx_MMPBSA**
   * https://g-mmpbsa.readthedocs.io/en/latest/install.html
   * calterlab (Kayla)
@@ Line 390: / Line 462: @@
 Installing collected packages: g_mmpbsa
 Successfully installed g_mmpbsa-3.0.9
+# works?
+ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+pygmtsar 2024.8.30.post3 requires pandas>=2.2, but you have pandas 1.5.3 which is incompatible.
+dask-expr 1.1.14 requires pandas>=2, but you have pandas 1.5.3 which is incompatible.
+xarray 2024.9.0 requires pandas>=2.1, but you have pandas 1.5.3 which is incompatible.
+Successfully installed gmx_MMPBSA-1.6.4 matplotlib-3.7.3 mpi4py-4.0.1 numpy-1.26.4 pandas-1.5.3 parmed-4.3.0 scipy-1.14.1 seaborn-0.11.2
+gmx-mmpbsa 1.6.4 requires pandas==1.5.3, but you have pandas 2.2.0 which is incompatible.
+Successfully installed pandas-2.2.0
+# back to
+Successfully installed pandas-1.5.3