search

DaehwanKimLab / tophat

Spliced read mapper for RNA-Seq
http://ccb.jhu.edu/software/tophat
Boost Software License 1.0
91 stars 46 forks source link

updated tarball (intervaltree, sortedcontainers), wrong install directory #22

Closed wookietreiber closed 8 years ago

wookietreiber commented 9 years ago

We at Arch Linux just realized that the tarball of 2.1.0 (http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz) got updated. We noticed, because the md5 of the tarball changed. Unfortunately, there was neither an update notice about this (which would have been ok) nor a version increment to 2.1.1 (which would have been better practice). Please do understand that these silent updates are bad open source software release practice. I (and I expect most people of the community would agree with me) would like to have a more open release practice in the future.

Apparently, from looking at the diff of the old and new tarballs, the Python packages intervaltree and sortedcontainers where originally missing and got added by this change.

The current version of the tarball installs these Python packages to $(DESTDIR)$(bindir) which is not the correct install location for Python packages on Linux / Unix distributions. Instead they should be installed to the site-packages directory of the used Python version that is detected via the PYTHON environment variable that is picked up during configure (most OS's of today ship with both Python 2 and Python 3).

gpertea commented 8 years ago

While in principle I agree with these points, we'd like to consider an exception for the last one - the distribution of intervaltree and sortedcontainers code, as some users might not be able to handle installation of Python modules in a commonsite-packages area - we wanted to provide a somewhat standalone, encapsulated install for regular users, yet with the ability to easily convert it to a common installation if needed..