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--- wiki:software:mb668 [2024/03/20 15:04] – keistc
+++ wiki:software:mb668 [2024/03/20 15:20] (current) – keistc
@@ Line 2: / Line 2: @@
 This class required numerous packages to download and compile.
 a list of software that we will need to run for the computing labs:
-  * R and Rscript Already installed in the docker image.\
+  * R and Rscript Already installed in the docker image.
   * [[https://github.com/BenLangmead/bowtie2|Bowtie2]] Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder.
   * [[https://github.com/samtools/samtools/releases/|SAMtools]] Download the source file.  Then ./configure --prefix=/home/.hub_local, make, make install
@@ Line 34: / Line 34: @@
   mkdir build ; cd build && cmake -DCMAKE_INSTALL_PREFIX=/home/.hub_local ..
   make
 This will get the metabat1 and metabat2 compiled. But failed after that. Will see if the rest is needed.
+  * [[https://github.com/Ecogenomics/CheckM/wiki/Installation|CheckM]] Follow link and use the pip3 install instructions using the hubpip command.  Python packages numby, matplotlib are already installed.
+  * [[https://github.com/broadinstitute/picard/releases|picard]] Download the latest version that will run with the version of Java on the hub. Version 2.27.4 worked on the current hub. Placed the jar file in the hub_data_share folder. To test run: java -jar picard.jar -h