Closed bocajnotnef closed 9 years ago
Also, trinity installation fails:
from 3-big-assembly.out
:
+ set -e
+ rm -fr /root/trinity.tar.gz '/root/bowtie*' '/root/samtools*'
+ rm -fr /mnt/work/trinity_out_dir
+ rm -f '/mnt/work/*.1' '/mnt/work/*.2'
++ date
+ echo 3-big-assembly compileTrinity Sat Mar 7 22:28:25 CST 2015
+ cd /root
+ curl -L 'http://sourceforge.net/projects/trinityrnaseq/files/latest/download?source=files'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0^M 0 407 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
^M 0 321 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
^M100 125 100 125 0 0 364 0 --:--:-- --:--:-- --:--:-- 364
+ tar xzf trinity.tar.gz
gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
``
Fix to be backported from master:
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.4.tar.gz \
-O trinity.tar.gz
tar xzf trinity.tar.gz
cd trinityrnaseq*/
make |& tee trinity-build.log
Closed #156
https://github.com/ged-lab/khmer-protocols/blob/master/mrnaseq/1-quality.txt#L48
needs || true appended, for situations where this is a clean environment. Otherwise the entire test breaks.