<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The conda installation of RepeatMasker runs oddly. It does not appear to run the ./configure script during setup, and is missing files inside the repeat library as a result.<div class=""><br class=""></div><div class="">--Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 4, 2019, at 2:00 AM, Lior Glick <<a href="mailto:liorglck@gmail.com" class="">liorglck@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear MAKER users,<div class=""><br class=""></div><div class="">I've been using MAKER for a while now, with RepeatMasker installed locally. By that I mean that I can type 'RepeatMasker' in my terminal and the software is initiated. Typing 'which RepeatMasker' shows the correct local path.</div><div class="">I also use this path as value for the maker_exe.ctl parameter 'RepeatMasker'.</div><div class="">Trying to generalize my working environment, I am trying to use a<a href="https://anaconda.org/bioconda/maker" class=""> conda env</a> which is capable of running MAKER. This env comes with RepeatMasker as well. Once I activate this env, I can still run RepeatMasker, but it points to a different path. When I run MAKER within this env, it fails right away with the error message:</div><div class="">ERROR: Could not determine if RepBase is installed<br class=""></div><div class="">Running the same configuration files locally (i.e. outside the conda env) results in a successful run.</div><div class="">This leads me to think that MAKER is not actually using the path indicated in the maker_exe.ctl file, and rather looks for RepeatMasker in $PATH or something similar. Is that the expected behavior? Any suggestions of how to overcome this issue?</div><div class=""><br class=""></div><div class="">Thanks and best regards,</div><div class="">Lior</div></div></div></div>
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