Compilation error linked to commit 7423f1c and 7599f22

[jsgounot]

Error reported first in issue #48.

Last two commits modified Contig.cpp, Contig.h, contig.cpp and contig.h in the git directory. This is due to macOS not managing properly files with same name but with case difference as explained here. I tried to revert these changes in my initial commit with last commit but this does not works.

Leads to a compilation error which ends like this:

make[1]: Entering directory '/home/ubuntu/TEMP/tmp/Release1/SHORT_READ_ANALYSIS/src'
make[1]: *** No rule to make target 'Contig.h', needed by 'ContigConverter.o'.  Stop.
make[1]: Leaving directory '/home/ubuntu/TEMP/tmp/Release1/SHORT_READ_ANALYSIS/src'
make: *** [Makefile:18: short_read_analysis] Error 2

Short fix: Reverting the modifications from a linux distribution and push. This will however not resolve the issue of people on mac OS installing OPERA-MS (if any).
Long fix: Modify contig or Contig files with different name.

[jsgounot]

The error should have been fixed with the last commit. If you've been affected, please update to last version. Let me know here if you have a similar compilation error.

For compilation errors which are not linked to this particular issue, please open a new github issue.

@drelo: Could you please confirm that the patch works on your side? Thanks a lot!

[drelo]

Hi again, I compiled with no errors. Next within the text_files folder I executed the test

perl ../OPERA-MS.pl \
    --contig-file contigs.fasta \
    --short-read1 R1.fastq.gz \
    --short-read2 R2.fastq.gz \
    --long-read long_read.fastq \
    --no-ref-clustering \
    --out-dir RESULTS 2> log.err

But I got this error

mkdir -p /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files

mkdir -p /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS/
version v0.9.0
mkdir -p /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/user_assembly

mkdir -p /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping

/mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/perl /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//OPERA-LG/bin//OPERA-long-read.pl --contig-file /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/user_assembly/contigs.fasta --kmer 60 --long-read-file /mnt/cive/exit/hassembly/OPERA-MS/test_files/long_read.fastq --output-prefix opera --output-directory /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping --num-of-processors 2 --opera /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//OPERA-LG/bin/ --illumina-read1 /mnt/cive/exit/hassembly/OPERA-MS/test_files/R1.fastq.gz --illumina-read2 /mnt/cive/exit/hassembly/OPERA-MS/test_files/R2.fastq.gz --samtools-dir /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/ --perl-dir /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/ --blasr /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/ --short-read-tooldir /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/ --skip-opera 1  --skip-short-read-mapping 1 > /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping/OPERA-long-read.out  2> /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping/OPERA-long-read.err
Error in the long read processing. Please see log for details /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping/OPERA-long-read.out /mnt/cive/exit/hassembly/OPERA-MS/test_files/RESULTS//intermediate_files/read_mapping/OPERA-long-read.err.

The.outis empty and the.errfile is just this line it seems the path to tools_opera has an extra "/" or maybe it is something else, let me know if you need additional info.
sh: /mnt/cive/exit/hassembly/OPERA-MS/test_files/..//tools_opera_ms/perl: No such file or directory

Thanks for your help!

[jsgounot]

Right ... this is something I forgot and should fix too. Meanwhile when you're sure you've activated the conda environment, you can make a quick temporary fix by creating a symlink: ln -s $(which perl) tools_opera_ms/perl. Sorry again by that.