diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 46769c6cc4c6c501e9b51a0713b264b12d05fd31..80f6ecc8feda8a5dc327491685e079a9e93f09f5 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/docs/SOP_alignment_variant_annotation.md
@@ -18,12 +18,10 @@ To generate the target BED file, first copy the file Twist_Exome_RefSeq_targets_
 
 ```
 cd /home/u035/project/resources
+source ../scripts/trio_whole_exome_config.sh
 
-../software/bcbio/bin/bedtools slop -g \
-  ../software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa.fai \
-  -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
-  ../software/bcbio/bin/bedtools merge > \
-  Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+bedtools slop -g $REFERENCE_GENOME.fai -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
+  bedtools merge > Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
 ```
 
 ## Input
@@ -96,7 +94,7 @@ OUTPUT_DIR=$BASE/output
 
 ARCHIVE_DIR=/archive/u035/trio_whole_exome
 
-export PATH=/home/u035/project/software/bcbio/bin:$PATH
+export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
 ````
 
 ## Template for bcbio configuration
diff --git a/docs/SOP_archiving.md b/docs/SOP_archiving.md
index ddf72557bd128e9286aead24c8695bf2ebbda758..38eb27d610dd934afe8a6e347bb401afe4b5699b 100644
--- a/docs/SOP_archiving.md
+++ b/docs/SOP_archiving.md
@@ -8,7 +8,7 @@ The user will need an account on the EPCC Ultra system. Contact Donald Scobbie (
 
 ## Software requirements
 
-Htslib 1.9 and Samtools 1.9 are installed at /home/u035/project/software/bcbio/bin.
+Htslib 1.9 and Samtools 1.9 are installed at /home/u035/project/software/bcbio/tools/bin.
 
 ## Data requirements
 
diff --git a/docs/SOP_sample_transfer_from_EdGe_to_EPCC.md b/docs/SOP_sample_transfer_from_EdGe_to_EPCC.md
index 7122b590df524c7879934aa954ce3d2fe3828a62..4b7bfb88a88d4fa5b88c1f2e85ce0b660912cbb1 100644
--- a/docs/SOP_sample_transfer_from_EdGe_to_EPCC.md
+++ b/docs/SOP_sample_transfer_from_EdGe_to_EPCC.md
@@ -22,7 +22,7 @@ This script will be referred to as <user_transfer_info_file>.
 
 ## Software requirements
 
-The Aspera command line interface software (version 3.7.4.147727) is installed in the project area at /home/u035/project/software/aspera/connect/bin. Md5 checksums are calculated by the system function md5sum. GNU Parallels is installed at /home/u035/project/software/bin.
+The Aspera command line interface software (version 3.7.4.147727) is installed in the project area at /home/u035/project/software/aspera/connect/bin. Md5 checksums are calculated by the system function md5sum.
 
 ## Notes
 
@@ -49,7 +49,7 @@ a.	The script is set to request 24 hours of wall time. The transfer speed is rou
 b.	If a download does not complete, this step may be run again and the download will resume from where it left off. If there are any files with extension .partial in the target directory, the download did not complete.
 
 ```
-cd /home/u035/project/trio_whole_exome/logs
+cd /scratch/u035/project/trio_whole_exome/logs
 project_id=<EdGE_project_id>
 transfer_sh=<full_path_to_user_transfer_info_file>
 qsub -v TRANSFER_INFO_FILE=$transfer_sh,PROJECT=$project_id \
@@ -68,7 +68,7 @@ If any files in a download do not have the correct md5 checksum, manually delete
 5. Clean up the logs directory.
 
 ```
-cd /home/u035/project/trio_whole_exome/logs
+cd /scratch/u035/project/trio_whole_exome/logs
 mv aspera.$project_id.* complete/
 mv project/$project_id.log complete/
 ```
diff --git a/docs/Software_installation.md b/docs/Software_installation.md
index f214d88bb7723aa1fa586f5acc87a0e857ca694f..c14bbd5602661cc797b8809e2b9aad7de27f6be4 100644
--- a/docs/Software_installation.md
+++ b/docs/Software_installation.md
@@ -15,7 +15,7 @@ wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_ins
 ulimit -n 4096
 
 python bcbio_nextgen_install.py /home/u035/project/software/bcbio \
-  --tooldir /home/u035/project/software/bcbio/bin \
+  --tooldir /home/u035/project/software/bcbio/tools \
   --genomes hg38 --aligners bwa \
   --datatarget variation --datatarget gnomad \
   --datatarget vep --datatarget dbnsfp --cores 32 &> bcbio_install_YYYYMMDDhhmm.log