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--- conda [2022/02/01 17:38] – jpummil
+++ conda [2025/10/15 19:51] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-==== Conda ====
+==== Conda Package Manager====
-==Conda==
+===Conda===
 [[http://https://docs.conda.io/en/latest/|Conda]] is an open source package management system and environment management system. Conda as a package manager helps you find and install packages. If you need a package that requires a different version of Python, you do not need to switch to a different environment manager, because conda is also an environment manager. With just a few commands, you can set up a totally separate environment to run that different version of Python, while continuing to run your usual version of Python in your normal environment.
@@ Line 14: / Line 14: @@
 <code>
-$ module load python/anaconda-3.8
+$ module load python/anaconda-3.14
-$ source /share/apps/bin/conda-3.8.sh
 </code>
@@ Line 26: / Line 25: @@
 conda config --add channels conda-forge
 </code>
+With everything above resolved, one can now search for relevant software that might be useful for their research...
+(*The following two commands should be done on a compute node as login nodes no longer have reliable access to the outside world.)
+<code>
+conda search <package name>
+</code>
+Once you find the package you wish to install, you would use the following example to perform the following task:
+<code>
+conda create -n <EnvName> <package name>
+</code>
+One may also use the following command to see what environments are already installed on Pinnacle and activate if suitable:
+<code>
+conda env list
+</code>
+As most users will utilize their new software installs in conjunction with a SLURM job script, below is a quick example of how this process would be implemented:
+<code>
+#SBATCH -J <EnvName>
+#SBATCH --partition comp06
+#SBATCH -o <EnvName>_%j.txt
+#SBATCH -e <EnvName>_%j.err
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=<userid>@uark.edu
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=32
+#SBATCH --time=06:00:00
+export OMP_NUM_THREADS=32
+module load python/anaconda-3.14
+conda activate <EnvName>
+</code>
+The Anaconda group maintain a very helpful "Cheat Sheet" for all things conda. If you have further questions, you can find it here: [[https://docs.google.com/viewer?url=https%3A%2F%2Fdocs.conda.io%2Fprojects%2Fconda%2Fen%2F4.6.0%2F_downloads%2F52a95608c49671267e40c689e0bc00ca%2Fconda-cheatsheet.pdf|Conda Cheat Sheet]]
@@ Line 31: / Line 68: @@
   * If a “conda install xxx” asks you to downgrade or revert anything…STOP! Don’t do it. In this case, create a unique environment for that specific software tool alone.
-  * If it says “requires Python 2.7”….we’d also just create an isolated environment.
+  * If it says “requires Python 2.7”….we’d also just create an isolated environment as python 2.x versions are no longer supported by the community.
-  * If “conda install xxx” shows just an enormous number of dependencies (Rstudio, BUSCO, and Qiime are prime examples)…best to Google before installing. These occasionally have “gotcha’s” that require a bit of additional effort.
+  * If “conda install xxx” shows just an enormous number of dependencies (Rstudio, BUSCO, GATK, and Qiime are prime examples)…best to Google before installing. These occasionally have “gotcha’s” that require a bit of additional effort.
   * Check developer page to see what the most current version of the software you need is…on occasion, the latest version on conda will be a couple of releases behind.
   * Though the situation improves daily, not ALL software packages are available thru conda repositories.
+  * While conda does make GPU accelerated packages available, it isn't as straightforward getting those to run properly due to the necessity of activating the appropriate NVIDIA run time tools.