Skipping dev tools upgrade - fixed in v1.2.8 bcbio

docs/Software_installation_ultra2.md

@@ -32,20 +32,11 @@ python3 bcbio_nextgen_install.py /home/u035/u035/shared/software/bcbio \
   --cores 128 &> bcbio_install_logs/bcbio_install_base_${DATE}.log
 ```
 
-Note: this could be fixed in version 1.2.8. Check htslib version after base install.
-
-Fix an issue with bcbio & vt/samtools/htslib. See https://github.com/bcbio/bcbio-nextgen/issues/3327 and https://github.com/bcbio/bcbio-nextgen/issues/3328.
-
-```
-DATE=`date +%Y%m%d%H%M`
-/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u development --tools &> bcbio_install_logs/bcbio_install_upgrade_tools_${DATE}.log
-```
-
 Install datatarget vep
 
 ```
 DATE=`date +%Y%m%d%H%M`
-/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_logs/bcbio_install_datatarget_vep_${DATE}.log
+/home/u035/u035/shared/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_logs/bcbio_install_datatarget_vep_${DATE}.log
 ```
 
 Q: do we even need gnomAD annotations on these? Should I be skipping VEP altogether for the alignment & variant calling pipeline?