zip file into tool_shed and install this tool through terminal command. This may means I do not install samtools, thus I download samtools and put this.

The most intensive SAMtools commands (samtools view, samtools sort) are multi-threaded, and therefore. bgzf_check_EOF: Invalid argument Galaxy attempted to build the BAM index with samtools 1.0+ but failed: No such file or directory: '/Users/biowzmailustceducn/galaxy/database/job_working_directory/000/40/_dataset_43_metadata_temp_file_b5rEcP.bai' /configure & make & sudo make install for the Mac. (ERR): hisat-align died with signal 6 (ABRT) Libc++abi.dylib: terminating with uncaught exception of type int Samtools: error closing standard output: -1 But when using samtools, I always get an error, the library file of samtools is not. Samtools: writing to standard output failed: Broken pipe Problem Description: I installed the samtools software with conda. o Write final output to stdout rather than Similar to corresponding options above f Use as full final filename rather than prefix

Specifically, we shall install the bioinformatics package SAMtools into a. T PREFIX Write temporary files to -T is INT Set number of sorting and compression threads This is done by installing the tools in a Docker container and then describ. O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or o FILE Write final output to FILE rather than standard output m INT Set maximum memory per thread suffix K/M/G recognized samtools software package provides processing sequence alignments in SAM and BAM formats, you can install in your Ubuntu 17.04 (Zesty Zapus) by running the. l INT Set compression level, from 0 (uncompressed) to 9 (best) The Conda installer takes care of other dependencies including Python itself. Select the appropriate path for something else. As an FYI based on the original poster, here is the full instructions for Noobs: Note that the installer for Conda is for the Python2.7, 64-bit version. When I used HISAT software, I met this error as follow: Dataset 33: HISAT on data 3Tool execution generated the following error message: Good direction to find an installer package for Samtools.

Samtools install