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cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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Move sync after chmod #31

Closed keiranmraine closed 5 years ago

keiranmraine commented 5 years ago

https://github.com/cancerit/dockstore-cgpwgs/issues/33

https://github.com/cancerit/PCAP-core/blob/develop/lib/PCAP/Threaded.pm#L294-L298

keiranmraine commented 5 years ago

Possibly just drop the chmod and change the following to execute with bash:

This: https://github.com/cancerit/PCAP-core/blob/693141eccdf9184ca087ef4d6bf15c695cd4d339/lib/PCAP/Threaded.pm#L268

To:

system("/usr/bin/time bash $script 1> $out 2> $err");
keiranmraine commented 5 years ago

Done in e8a6b2c22fe06fc570647b5c45ff37cac75bb3b3

keiranmraine commented 5 years ago

Fixed in V4.2.7.