HISAT2 2.0.5 update

tor · 02-14-2017, 08:31 AM

Since NCBI change a policy (HTTP to HTTPS) in using SRA data, HISAT2 was updated to version 2.0.5. I have HISAT2 2.0.1 installed with homebrew.

I want to update it to the latest version downloaded from the site (source code) and want to add NCBI-NGS support (to work directly with SRA files).
According to the instructions I should use make with next options

"make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options.
For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used."

However, when I checked the ngs directory in /usr/local/ I found that directory /include and /lib64 located under /usr/local/ngs/ngs-sdk

I have two questions.
1. If I install the HISAT2 from the source, what will happen to simlinks from homebrew installation?
2. Should I use actual path to the directory /include and /lib64 or I can use the path to directory /ngs ?
Thank you

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02-14-2017, 08:31 AM	#1
tor Junior Member Location: NY Join Date: Feb 2017 Posts: 1	HISAT2 2.0.5 update Since NCBI change a policy (HTTP to HTTPS) in using SRA data, HISAT2 was updated to version 2.0.5. I have HISAT2 2.0.1 installed with homebrew. I want to update it to the latest version downloaded from the site (source code) and want to add NCBI-NGS support (to work directly with SRA files). According to the instructions I should use make with next options "make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options. For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used." However, when I checked the ngs directory in /usr/local/ I found that directory /include and /lib64 located under /usr/local/ngs/ngs-sdk I have two questions. 1. If I install the HISAT2 from the source, what will happen to simlinks from homebrew installation? 2. Should I use actual path to the directory /include and /lib64 or I can use the path to directory /ngs ? Thank you