lumpy_filter missing / never built

[jbsysadmin]

Greetings. I tried to install lumpy-sv v0.2.13 (for smoove-0.2.3). All dependencies are met, except one. When calling smoove, I see "lumpy_filter" is missing. The build instructions here make no direct allowance for lumpy_filter. There is nothing related to that in the resulting, in-place build tree. Was something needed beyond "make" to compile lumpy_filter? Are there flags /switches missing from the install doc?

[EricDeveaud]

hello, same reasons (smoove) abd same problem here unfortunatly the v0.2.13 tag release does not contains the lumpy_filter code. (check src directory form archive versus src directory from git clone)

I was abble to fix the problem

wget https://raw.githubusercontent.com/arq5x/lumpy-sv/master/src/filter/filter.c
module load htslib/1.9
gcc gcc -o lumpy_filter filter.c -lcrypto -lcurl -lpthread -lz -lhts

if you don't have htslib available as a module, 1) find where libhts.so is on your system eg /somehere/lib/libhts.so and note the parent directory name, => /somehere/lib 2) find where htslib/sam.h is located on your system eg /somehere/include/htslib/sam.h and note the parent directory ==> /somehere/include/

then compile this way

gcc gcc -Isomehere/include -L/somehere/lib -o lumpy_filter filter.c -lcrypto -lcurl -lpthread -lz -lhts

[jbsysadmin]

Thanks. I forgot to post: please close ticket. Issues were that I needed “all” target, and that I needed the latest lumpy (reported by smoove support.) I think the direct download link pointed to an older version.

git clone https://github.com/arq5x/lumpy-sv.git cd lumpy-sv make all

-John

From: Eric Deveaud notifications@github.com Sent: Wednesday, February 13, 2019 10:46 AM To: arq5x/lumpy-sv lumpy-sv@noreply.github.com Cc: Burns, W. J. wjb2130@cumc.columbia.edu; Author author@noreply.github.com Subject: Re: [arq5x/lumpy-sv] lumpy_filter missing / never built (#289)

hello, same reasons (smoove) abd same problem here unfortunatly the v0.2.13 tag release does not contains the lumpy_filter code. (check src directory form archive versus src directory from git clone)

I was abble to fix the problem

wget https://raw.githubusercontent.com/arq5x/lumpy-sv/master/src/filter/filter.c

module load htslib/1.9

gcc gcc -o lumpy_filter filter.c -lcrypto -lcurl -lpthread -lz -lhts

if you don't have htslib available as a module,

1. find where libhts.so is on your system eg /somehere/lib/libhts.so and note the parent directory name, => /somehere/lib
2. find where htslib/sam.h is located on your system eg /somehere/include/htslib/sam.h and note the parent directory ==> /somehere/include/

then compile this way

gcc gcc -Isomehere/include -L/somehere/lib -o lumpy_filter filter.c -lcrypto -lcurl -lpthread -lz -lhts

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