# Bwa-mem2 data manager??? **URL:** \ **Category:** Uncategorized\ **Tags:** reference-index, galaxy-local, bwa\_mem2\ **Created:** [February 16, 2024, 6:39pm UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727 "2024-02-16T18:39:56Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![KaunoSeptintasFortas](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kaunoseptintasfortas/32/5149_2.png) [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)\ **Post date:** [February 16, 2024, 6:39pm UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727/1 "2024-02-16T18:39:56Z")
Hello, Bwa-mem2 is presented in toolshed for local Galaxy install, but I cannot find it`s data manager to build indexes. How can I start bwa-mem2 on local Galaxy? Thank you. ---
**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\ **Post date:** [February 17, 2024, 4:54am UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727/2 "2024-02-17T04:54:09Z")
The tool itself (bwa-mem2) can build an index from a fasta in your history. If you want prebuilt indeces you can mount our distributed filesystem – [Hands-on: Hands-on: Reference Data with CVMFS without Ansible / Galaxy Server administration](https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs-manual/tutorial.html) You can also put those indeces in data tables by hand. ---
**Author:** ![KaunoSeptintasFortas](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kaunoseptintasfortas/32/5149_2.png) [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)\ **Post date:** [February 18, 2024, 3:38pm UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727/3 "2024-02-18T15:38:55Z")
Problem was solved in such a way: 1. Install bwa-mem2 just as independent conda package in linux environment and build indexes. You should have such a files for HG19 genome: hg19.fa.pac hg19.fa.bwt.2bit.64 hg19.fa.ann hg19.fa.amb hg19.fa.0123 hg19.fa Put this file in directory accessible for galaxy and edit/create bwa\_mem2\_index.loc in the same manner as it is for bwa-mem. I needed to restart not only galaxy, but all server because of some hunged galaxy tasks from the past. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2026, 4:43am UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727/4 "2026-03-17T04:43:55Z")