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| author | Pjotr Prins | 2021-09-17 03:21:01 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2021-09-17 03:21:01 -0500 |
| commit | 194be64cf1b1b3ee224cba7312c76d835a77cbc8 (patch) | |
| tree | 77d8b57cb6748029bf7bd526e5c4b7c19a8bc463 /issues | |
| parent | a9278803669bf989a96c20fe51fe0d48a447ce47 (diff) | |
| download | gn-gemtext-194be64cf1b1b3ee224cba7312c76d835a77cbc8.tar.gz | |
Comment on pairscan for efraimf
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/genenetwork1/gn1-pairscan.gmi | 17 |
1 files changed, 15 insertions, 2 deletions
diff --git a/issues/genenetwork1/gn1-pairscan.gmi b/issues/genenetwork1/gn1-pairscan.gmi index a47a3a3..9d90bc1 100644 --- a/issues/genenetwork1/gn1-pairscan.gmi +++ b/issues/genenetwork1/gn1-pairscan.gmi @@ -16,6 +16,8 @@ ImportError: No module named direct # Tags * critical bug +* missing dependency +* binary blob * assigned: pjotrp # Notes @@ -54,8 +56,6 @@ First update guix with gn1@tux01:~$ ~/opt/guix/bin/guix pull -p ~/opt/guix-latest ``` -Which got me the error Unbound variable: license:bsd-0. - followed by the git repos above. The error changed into @@ -68,3 +68,16 @@ Traceback (most recent call last): ResultFull, ResultInteract, ResultAdd = direct.permu(webqtlConfig.GENODIR, _vals, _strains, genofile + ".geno", 500) #XZ, 08/14/2008: add module name webqtlConfig AttributeError: 'module' object has no attribute 'permu' ``` + +Turns out we are using the wrong direct.so. I made it work by adding the binary blob with LD_LIBRARY_PATH (also required libstdc++.so.6) + +* assigned: efraimf + +I just fixed pairscan with a bad hack. You can enjoy the production +machine. Note it will disappear on a restart right now of GN1. Efraim, +it works if direct.so and libstdc++.so.6 are visible. Maybe you can +add the binary blob to GN1 and we pray it keeps working? + +With gn1.genenetwork.org test by selecting the hippocampus dataset, +look for 'shh' gene, click 'pair scan' on the mapping page and +'compute'. |