cusbg / traveler Goto Github PK

Thanks again for the great software!

One of the required inputs is a FASTA file with the sequence and structure of the template. It wasn't immediately clear to me how to get these files in a (semi)automatic way, so I ended up downloading the CRW structures in bpseq format and then converting bpseq to FASTA using the RNApdbee web service.

I have 2 questions:

1. Is there a better way to get the template FASTA files?
2. Could Traveler take the bpseq files as an input to avoid the conversion process?

Thank you for looking into this!

it is a great tool. however, when I installed it, no matter manually or docker, it come to errors.

$ sudo docker build . -t traveler
Sending build context to Docker daemon 188.9MB
Step 1/6 : FROM gcc:4.9
4.9: Pulling from library/gcc
aa18ad1a0d33: Pull complete
15a33158a136: Pull complete
f67323742a64: Pull complete
c4b45e832c38: Pull complete
e5d4afe2cf59: Pull complete
1efbd2d5674a: Pull complete
022a58c161f7: Pull complete
6461d3be7619: Pull complete
Digest: sha256:6356ef8b29cc3522527a85b6c58a28626744514bea87a10ff2bf67599a7474f5
Status: Downloaded newer image for gcc:4.9
---> 1b3de68a7ff8
Step 2/6 : COPY . /usr/src/traveler
---> 1f3a3437c11d
Step 3/6 : WORKDIR /usr/src/traveler
---> Running in 6f2f6e21bcc4
Removing intermediate container 6f2f6e21bcc4
---> e4284f819730
Step 4/6 : RUN cd /usr/src/traveler/src && make build
---> Running in 60cadef29f9c
MAKEFILE-GENERATING:tree

make --directory=tree --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/tree'
make[1]: Leaving directory '/usr/src/traveler/src/tree'

END-MAKEFILE-GENERATING:tree
MAKEFILE-GENERATING:ted

make --directory=ted --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/ted'
make[1]: Leaving directory '/usr/src/traveler/src/ted'

END-MAKEFILE-GENERATING:ted
MAKEFILE-GENERATING:utils

make --directory=utils --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/utils'
make[1]: Leaving directory '/usr/src/traveler/src/utils'

END-MAKEFILE-GENERATING:utils
MAKEFILE-GENERATING:draw

make --directory=draw --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/draw'
make[1]: Leaving directory '/usr/src/traveler/src/draw'

END-MAKEFILE-GENERATING:draw
MAKEFILE-GENERATING:app

make --directory=app --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/app'
make[1]: Leaving directory '/usr/src/traveler/src/app'

END-MAKEFILE-GENERATING:app
MAKEFILE-GENERATING:tests

make --directory=tests --makefile=Makefile make
make[1]: Entering directory '/usr/src/traveler/src/tests'
make[1]: Leaving directory '/usr/src/traveler/src/tests'

END-MAKEFILE-GENERATING:tests
COMPILE:

make -j2 --directory=./build -f Makefile build
make[1]: Entering directory '/usr/src/traveler/src/build'
g++ -std=gnu++11 -c -g -Wall -I../include/ -I../include/tests/ -DLOG_FILE="/tmp/traveler.log" ../utils/document_writer.cpp -o document_writer.o
g++ -std=gnu++11 -c -g -Wall -I../include/ -I../include/tests/ -DLOG_FILE="/tmp/traveler.log" ../utils/logger.cpp -o logger.o
../utils/document_writer.cpp: In member function 'std::string document_writer::get_rna_background_formatted(tree_base<rna_pair_label>::pre_post_order_iterator, tree_base<rna_pair_label>::pre_post_order_iterator) const':
../utils/document_writer.cpp:425:35: error: 'f' was not declared in this scope
point diff_orig = p2 - p1;f
^
../utils/document_writer.cpp:429:14: error: 'tmp' was not declared in this scope
p1 = tmp;
^
g++ -std=gnu++11 -c -g -Wall -I../include/ -I../include/tests/ -DLOG_FILE="/tmp/traveler.log" ../utils/ps_writer.cpp -o ps_writer.o
document_writer.cpp.mk:9: recipe for target 'document_writer.o' failed
make[1]: *** [document_writer.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/usr/src/traveler/src/build'
Makefile:33: recipe for target 'compile' failed
make: *** [compile] Error 2
The command '/bin/sh -c cd /usr/src/traveler/src && make build' returned a non-zero code: 2

could you give me some suggestions on how to deal with it?

My best,

Minglei

Hi!
I met an install error.
I ran this command:

git clone https://github.com/davidhoksza/traveler
cd traveler/src
make build

and, the error is:

****************MAKEFILE-GENERATING:tree****************

make --directory=tree --makefile=Makefile make
make[1]: *** No rule to make target `../build//rna_tree_label.cpp.mk', needed by `make'.  Stop.
make: *** [tree] Error 2

I am using the following env:
OS: macOS High Sierra 10.13.6
gcc (GCC): 4.8.5
GNU Make: 3.81

I couldn't understand why this error happened. Is the problem in my env?
I would appreciate if you know how to solve this.

Best regards,
Shunsuke

This looks awesome. I'll install it manually for now, but it makes like a ton easier when there's a prebuilt version I can rely on and download easily.