ababaian / serratus

Ultra-deep search for novel viruses
http://serratus.io
GNU General Public License v3.0
250 stars 32 forks source link

New Base Image added for use in Dockerfile #253

Open thesharmanitish opened 2 years ago

thesharmanitish commented 2 years ago

Step1: build Dockerfile_BaseImg Step 2: Build Dockerfile

Currently Dockerfile is failing in last step with below error. I need to check the source code of gappa to understand furthur the root cause.

[ 2%] Building CXX object libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/////genesis_unity_sources/lib/all.cpp.o /gappa/build/genesis_unitysources/lib/all.cpp: In function 'std::string genesis::utils::strerror()': /gappa/build/genesis_unity_sources/lib/all.cpp:36523:41: error: invalid conversion from 'int' to 'const char*' [-fpermissive] 36523 std::string tmp(p, std::strlen( p )); ^
int

In file included from /usr/include/fortify/wchar.h:30, from /usr/include/c++/10.3.1/cwchar:44, from /usr/include/c++/10.3.1/bits/postypes.h:40, from /usr/include/c++/10.3.1/iosfwd:40, from /usr/include/c++/10.3.1/memory:74, from /gappa/libs/genesis/lib/genesis/placement/sample.hpp:34, from /gappa/libs/genesis/lib/genesis/placement/function/helper.hpp:34, from /gappa/build/genesis_unity_sources/lib/all.cpp:33: /usr/include/string.h:52:16: note: initializing argument 1 of 'size_t strlen(const char)' 52 | size_t strlen (const char ); | ^~~~ make[3]: [libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/build.make:76: libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/////genesis_unity_sources/lib/all.cpp.o] Error 1 make[2]: [CMakeFiles/Makefile2:141: libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/all] Error 2 make[1]: [Makefile:91: all] Error 2 make: [Makefile:44: build] Error 2

ababaian commented 2 years ago

Sorry I forgot to mention, the containers which need optimization are: serratus-dl, serratus-align and serratus-merge. Those are the ones which are deployed 10,000's of times during a run. Most of the others are used occasionally and do not need to be optimized to high scale currently.

rednitish commented 2 years ago

No problem, I will take a look at them as well, Meanwhile can you please review this as well, If it requires some changes let me know,