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--- cluster:73 [2021/12/06 15:51]
hmeij07 [Hoomd]
+++ cluster:73 [2022/04/01 14:09]
hmeij07 [Paleogenomics Tools]
@@ Line 19: / Line 19: @@
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== HPC SDK ======
+    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:212
+    * Nvidia SDK v 22.2
 ====== Magenta ======
@@ Line 597: / Line 602: @@
 </code>
+Added\\
+ --- //[[hmeij@wesleyan.edu|Henk]] 2022/01/03 14:35//\\
+# https://github.com/merenlab/anvio/issues/1479
+<code>
+conda install -c bioconda samtools=1.9 --force-reinstall
+The following NEW packages will be INSTALLED:
+  gettext            conda-forge/linux-64::gettext-0.19.8.1-hf34092f_1004
+  htslib             bioconda/linux-64::htslib-1.9-h4da6232_3
+  libdeflate         bioconda/linux-64::libdeflate-1.2-h516909a_1
+  libglib            conda-forge/linux-64::libglib-2.66.3-hbe7bbb4_0
+  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
+The following packages will be UPDATED:
+  cffi                pkgs/main::cffi-1.14.3-py38h261ae71_2 --> conda-forge::cffi-1.14.4-py38ha312104_0
+  libedit            pkgs/main::libedit-3.1.20191231-h14c3~ --> conda-forge::libedit-3.1.20191231-h46ee950_2
+  samtools                                            1.7-1 --> 1.9-h10a08f8_12
+The following packages will be SUPERSEDED by a higher-priority channel:
+  glib                    pkgs/main::glib-2.69.0-h5202010_0 --> conda-forge::glib-2.66.3-h58526e2_0
+  libffi                   pkgs/main::libffi-3.3-he6710b0_2 --> conda-forge::libffi-3.2.1-he1b5a44_1007
+  ncurses                 pkgs/main::ncurses-6.2-he6710b0_1 --> conda-forge::ncurses-6.1-hf484d3e_1002
+  python                 pkgs/main::python-3.8.5-h7579374_1 --> conda-forge::python-3.8.3-cpython_he5300dc_0
+  sqlite                pkgs/main::sqlite-3.33.0-h62c20be_0 --> conda-forge::sqlite-3.32.3-hcee41ef_1
+$ samtools --version
+samtools 1.9
+Using htslib 1.9
+Copyright (C) 2018 Genome Research Ltd.
+</code>
 ====== pytraj ======
@@ Line 648: / Line 692: @@
 ====== OpenHPC ======
-So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
+So I remember where I put the tar repo file
-  * whitetail tar ball for centos7/warewulf (no slurm)
+  * OpenHPC v2.4
-  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
+  * Rocky 8.5
-  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
+  * Slurm 20.11.8
-  * https://github.com/warewulf/warewulf3 (master git zip file)
+  * Warewulf 3.9
+  * x86_64
+<code>
+[root@cottontail2 ~]# ll /share/apps/src/cottontail2/openhpc/
+total 8290421
+-rw------- 1 root root     562276 Mar 17 09:34 Install_guide-Rocky8-Warewulf-SLURM-2.4-x86_64.pdf
+-rw-r--r-- 1 root root      10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm
+-rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
+</code>
 ====== OneAPI ======
@@ Line 864: / Line 919: @@
 </code>
+  * **mapDamage2**
+  * https://github.com/ginolhac/mapDamage/issues/25
+  * docker container is broke
+  * requires centos6 so queues hp12, mw128
+  * conda install -c 'bioconda' mapdamage2
+<code>
+# env
+export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
+export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
+The following NEW packages will be INSTALLED:
+  mapdamage2         bioconda/linux-64::mapdamage2-2.0.6-1
+  pysam              bioconda/linux-64::pysam-0.16.0.1-py27hc729bab_3
+  seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_3
+</code>
@@ Line 2958: / Line 3034: @@
   * https://edwards.sdsu.edu/research/c11-on-centos-6/
     * C11++ on CentOS6, two version of gcc
-    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''
+    * read the R-3.6.1_configure file in ''/share/apps/CENTOS6/R/R-3.6.1_configure''
 <code>

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