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| author | Muriithi Frederick Muriuki | 2021-08-26 07:41:48 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-26 07:41:48 +0300 |
| commit | ca4c5b5fc5c9f701183589ab0032790cee353248 (patch) | |
| tree | b98f60cae8be4924af92698f22461f8187d5c1d8 | |
| parent | ed4976304903e90d48256e185751daece3b77373 (diff) | |
| download | gn-gemtext-ca4c5b5fc5c9f701183589ab0032790cee353248.tar.gz | |
Update issue with findings on rust-qtlreaper
* The usage of ~rust-qtlreaper~ in GN2 is not quite clear. This commit
details the findings of the search for the usage of ~rust-qtlreaper~
in GN2 and the attempts to replicate in GN3.
| -rw-r--r-- | topics/gn1-migration-to-gn2/clustering.gmi | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/topics/gn1-migration-to-gn2/clustering.gmi b/topics/gn1-migration-to-gn2/clustering.gmi index 08b3686..6b88be3 100644 --- a/topics/gn1-migration-to-gn2/clustering.gmi +++ b/topics/gn1-migration-to-gn2/clustering.gmi @@ -225,3 +225,33 @@ The `neworder` variable setup has been partially migrated. The use of the `xoffs Also migrated retrieval of strains with non-NoneType values Awaiting response on use of QTLReaper. + +## 2021-08-26 + +Reading through the Genenetwork2 code to figure out how the ~rust-qtlreaper~ module is used. + +I cloned + +=> https://github.com/chfi/rust-qtlreaper ~rust-qtlreaper~ + +and searched through the code for python bindings (py_module_initializer!) but could not find it in either the rust-qtlreaper or genenetwork2 repositories + +This causes me to suspect that when ~import reaper~ appears in the Genenetwork2 code, it actually uses the older QTLReaper implemented in C. This suspicion is further strengthened by the fact that when + +=> https://github.com/genenetwork/genenetwork3/commit/7aa5f5422908b4dbfc80f3f73b008507878a34aa I added ~rust-qtlreaper~ + +to the dependencies for the Genenetwork3 environment, I could not do ~import reaper~ successfully: + +``` +$ env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm +frederick@galadriel-ubuntu ~/genenetwork/genenetwork3 [env]$ python3 +Python 3.8.2 (default, Jan 1 1970, 00:00:01) +[GCC 7.5.0] on linux +Type "help", "copyright", "credits" or "license" for more information. +>>> import reaper +Traceback (most recent call last): + File "<stdin>", line 1, in <module> +ModuleNotFoundError: No module named 'reaper' +``` + +There's a chance we might have to write a separate rust library whose entire purpose is to add the python bindings, or maybe add the bindings to the rust-qtlreaper library itself. |