Update mac documentation to include arm64 #330
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
martin-g
reviewed
Sep 26, 2023
| `openjdk-14.0.1_osx-x64_bin.tar.gz`) to `~/Downloads/`. | ||
| Go to https://jdk.java.net/ and follow the link to the latest JDK. Then | ||
| download the tarball for your specifc mac (e.g. `openjdk-18.0.1.1_macos-x64_bin.tar.gz` | ||
| or `openjdk-18.0.1.1_macos-aarch64_bin.tar.gz`) to `~/Downloads/`. |
There was a problem hiding this comment.
I'd recommend using https://adoptium.net/ instead. There one can easily find which is the latest LTS release. Currently it shows v17 but it will change to v21 in the coming days.
Java 18 is not supported any more.
There was a problem hiding this comment.
Thanks for the suggestion. I'll update the machines next month. Good to know Java needs an update.
| @@ -1320,6 +1358,8 @@ effect. Then: | |||
|
|
|||
| ### 4.6 Install Open Babel | |||
|
|
|||
| TODO: Modify instructions for arm64 | |||
|
|
|||
| The **ChemmineOB** package requires Open Babel 3. Note that the Open Babel | |||
| website seems very outdated: | |||
There was a problem hiding this comment.
I use the following steps to build OpenBabel for Linux ARM64:
wget https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/openbabel-3.1.1-source.tar.bz2
tar jxvf openbabel-3.1.1-source.tar.bz2
cd openbabel-3.1.1
mkdir build && cd build
cmake ..
make -j
export OPEN_BABEL_HOME="/home/biocbuild/openbabel-3.1.1"
cmake --install . --prefix $OPEN_BABEL_HOME
export OPENBABEL_CFLAGS="-I$OPEN_BABEL_HOME/include/openbabel3 -L$OPEN_BABEL_HOME/lib"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPEN_BABEL_HOME/lib
|
@martin-g Thanks for reviewing! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Close #283
Rather than make a separate document, I've included the information for configuring a mac arm64 with the x86_64 mac. There are two that should be updated for open babel (required by ChemmineOB) and ensemblVEP (required by ensemblVEP) as they appear to error on arm64 and this is tracked in #329.