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micans / mcl

MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.
https://micans.org/mcl
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installation of mcl-22-282.tar.gz with fatal error: tingea/types.h: No such file or directory #13

Closed azat-badretdin closed 1 year ago

azat-badretdin commented 1 year ago 
make[2]: Entering directory `/home/badrazat/mcl-22-282/src/clew'
gcc -DHAVE_CONFIG_H -I. -I../..  -I../../src -I../..   -g -O2 -pthread -MT scan.o -MD -MP -MF .deps/scan.Tpo -c -o scan.o scan.c
In file included from ../../src/impala/matrix.h:42:0,
                 from scan.h:61,
                 from scan.c:16:
../../src/impala/ivp.h:16:10: fatal error: tingea/types.h: No such file or directory
 #include "tingea/types.h"
          ^~~~~~~~~~~~~~~~

make install for the previous version mcl-14-137 is successful.

micans commented 1 year ago

Hi, mcl requires installation of a C utility library called cimfomfa (it provides e.g. tingea/types.h). See https://github.com/micans/mcl#mcl for an installation recipe - it centers around the script install-this-mcl.sh that can be found at the top level in this respository.

azat-badretdin commented 1 year ago

Thanks. My trajectory was from roary installation page https://github.com/sanger-pathogens/Roary/blob/master/README.md#required-dependencies which goes to https://micans.org/mcl/ which goes to https://micans.org/mcl/src

What is the best starting point for MCL? Maybe this info can be passed to roary folks.

micans commented 1 year ago

For Roary it may be best to go with mcl-14-137, as Roary depends on mclblastline. The latter is currently not shipped with 22-282, I will probably rectify this in the future. If you installed mcl-14-137 then you may already have mclblastline. A further note is that there is no difference between the mcl clustering programs between those two versions; the changes are more to do with sibling programs (notes are in ChangeLog). The upshot is (1) there is very unlikely to be an issue if you mixed versions of programs between the two releases, and (2) if you use mcl-14-137 to get mclblastline + mcl then that's fine too as mcl has only had cosmetic changes.

I know that Debian may ship mcl-22-282 and back-port mclblastline for it, but the release is pending for other reasons. The 22-282 version of mcl does bring some niggles such as the new and changed installation procedure with added issue of missing mclblasline. I'll try to rectify/document issues as best as I can where appropriate.

azat-badretdin commented 1 year ago

Thanks! I guess the issue can be closed...