cbBuild 0.25 fails with sample 1 data about cellbrowser HOT 8 CLOSED

On Tue, Sep 18, 2018 at 11:36 AM, Pablo Moreno ***@***.***> wrote: To follow up on this @maximilianh <https://github.com/maximilianh> I forked and tagged the last commit that was working fine (a20c4d0 <a20c4d0>) with 0.1.9, however I still get other errors... the only difference between this and the previous time that the container was built (unfortunately that container was lost due to some changes in our CI) with that version seem to be the version of some dependencies pulled by conda. Before it was numpy 1.14.3 and now 1.15.x. I pinned down to 1.14.3, but errors I get with 0.1.9 are: INFO:root:Copying+reordering+trimming /export/galaxy-central/database/files/000/dataset_42.dat to /export/galaxy-central/database/job_working_directory/000/40/dataset_45_files/sample/exprMatrix.tsv, keeping only the 4261 columns with a sample name in the meta data INFO:root:converting /export/galaxy-central/database/job_working_directory/000/40/dataset_45_files/sample/exprMatrix.tsv.gz to /export/galaxy-central/database/job_working_directory/000/40/dataset_45_files/sample/exprMatrix.bin and writing index to /export/galaxy-central/database/job_working_directory/000/40/dataset_45_files/sample/exprMatrix.json INFO:root:Compressing gene expression vectors... INFO:root:Auto-detecting number type of /export/galaxy-central/database/job_working_directory/000/40/dataset_45_files/sample/exprMatrix.tsv.gz INFO:root:Numbers in matrix are of type 'float' Traceback (most recent call last): File "/usr/local/bin/cbBuild", line 10, in <module> cellbrowser.convertAndCopyCli() File "/usr/local/bin/cbPyLib/cellbrowser.py", line 2145, in convertAndCopyCli convertAndCopy(confFnames, outDir, port) File "/usr/local/bin/cbPyLib/cellbrowser.py", line 2119, in convertAndCopy convertDataset(inConf, outConf, datasetDir) File "/usr/local/bin/cbPyLib/cellbrowser.py", line 1962, in convertDataset convertExprMatrix(inConf, outMatrixFname, outConf, sampleNames, geneToSym, datasetDir, needFilterMatrix) File "/usr/local/bin/cbPyLib/cellbrowser.py", line 1696, in convertExprMatrix matType = matrixToBin(outMatrixFname, geneToSym, binMat, binMatIndex, discretBinMat, discretMatrixIndex) File "/usr/local/bin/cbPyLib/cellbrowser.py", line 1035, in matrixToBin matType, sampleNames = matReader.open(fname) TypeError: 'NoneType' object is not iterable Any ideas? I'm happy to move to something above 0.25 again, but currently 0.25's cbBuild is not working either (see first comment above) :-(. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAS-TXXDpkWypxUCEnPa0kYxdQpXaws2ks5ucL6wgaJpZM4WstOW> .

On Tue, Sep 18, 2018 at 6:14 AM, Pablo Moreno ***@***.***> wrote: Ok, 0.25 works, this was a late night working error, apologies for the extra issue! Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAS-TTOHBnB8eyguBYeUGeTDuZ7egYJ4ks5ucMd7gaJpZM4WstOW> .

On Tue, Sep 18, 2018 at 6:18 AM, Pablo Moreno ***@***.***> wrote: Closed #25 <#25>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAS-TdCkKgk-hGsfXuq80vmnslIEPWL7ks5ucMh4gaJpZM4WstOW> .