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**Location - Both Linux and OSX use $HOME/.local to store application-specific files for each user. This standard has been around for many years. So let's put it there.
The question is where? Many applications seem to put everything in ./local/share, or .local/share/applications, but we need to find out exactly what the convention is. Whatever the directory, let's create a subdirectory called 'birch'.

NCBI API keys for Eutils

Background; To better regulate traffic from Eutils, Eutils requests are not processed if there are more than 3 requests in any 1 second window from a given IP address. Individual users can get an API key by getting a MyNCBI account. See
Why and how should I get an API key to use the E-utilities?

Problem: How do we make it easy for BIRCH users to get an API key, and how do we get BIRCH to use that key?


bldna, blprotein



We need a way to add phylogenetic information, and maybe other information, to phylogenetic trees, based on Accession number.

One approach is to use blastcmd eg.

{neptune:/home/psgendb/temp}blastdbcmd -entry AB005234 -db nt -outfmt %S,%N,%K
Arabidopsis thaliana,Arabidopsis thaliana,Eukaryota

The output from something like this could be used to add this information to a phyloXML file using the phylogeny decorator from the forester package. One problem with blastcmd is that by default it reads info from a local copy of a blast database. If you want to get the information from NCBI, you need an RID from a previous BLAST search. Also, blastdbcmd needs to be told which database to get the information from.

It may also be possible to do this using NCBI query. Is that true of Eutils?


Current version won't work for users who don't have write access to Jalview home directory. Question has been posted to asking if there is a workaround.
Solution: In addition to the installer, Jalview can also be obtained from their github as a single Jar file with the complete package. This is platform-independent, although the current version requires a Java 8 JRE. Since many systems now default to Java 11, the solution is to have a universal copy of the Jar file in $BIRCH/java, and a platform-specific Java 8 JRE in $BIRCH/lib-$BIRCH_PLATFORM. Run Jalview from a script that finds the JRE, and everything works. Future versions will be Java 11 compliant, and we should be able to do away with the JRE at that point.


host system status
CCL - BIRCHDEV RHEL7 completed
brassica - Fedora31-2 VM fedora 31 completed
brassica MATE Ubuntu 16 LTS complete
peacock MacOSX completed
maui Ubuntu MATE 18.0.4 LTS ND
wotan Scientific Linux 7 completed
flamingo Ubuntu MATE 18.0.4 LTS completed
triticum Ubuntu MATE 18.0.4 LTS completed
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