diff --git a/.nojekyll b/.nojekyll index 9efa341..32c89c4 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -4a188cda \ No newline at end of file +30cc38f6 \ No newline at end of file diff --git a/404.html b/404.html index 901b567..3e45aca 100644 --- a/404.html +++ b/404.html @@ -2,7 +2,7 @@
- + @@ -274,6 +274,24 @@Note, if you plan to use the Docker container or install via conda
/mamba
you can skip this section as all dependencies are wrapped up in these methods.
If you plan to use the Docker container or install via conda
/mamba
you can skip this section as all dependencies are wrapped up in these methods.
If you plan to compile your own copy of dupsifter
or run the pre-compiled binaries, there are several external dependencies that are needed:
zlib
@@ -258,16 +270,14 @@ libbz2Download and Install<
Precompiled Binaries
Precompiled binaries are available for macOS and Linux:
# macOS
-curl -OL $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest |
-grep browser_download_url | grep darwin_amd64 | cut -d '"' -f 4)
- mv dupsifter_* dupsifter
-chmod +x dupsifter
-
-# Linux
-curl -OL $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest |
-grep browser_download_url | grep linux_amd64 | cut -d '"' -f 4)
- mv dupsifter_* dupsifter
-chmod +x dupsifter
+curl -L $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest |
+grep browser_download_url | grep darwin_amd64 | cut -d '"' -f 4) --output dupsifter
+ chmod +x dupsifter
+
+# Linux
+curl -L $(curl -s https://api.github.com/repos/huishenlab/dupsifter/releases/latest |
+grep browser_download_url | grep linux_amd64 | cut -d '"' -f 4) --output dupsifter
+ chmod +x dupsifter
Short Option | -Long Option | +Long Option | Argument Type | Description |
---|---|---|---|---|
-o | -–output | +–output | string | Name of output file (either .sam or .bam) |
-O | -–stats-output | +–stats-output | string | Name of file to write statistics to (end with .dupsifter.stat ) |
-s | -–single-end | +–single-end | none | Run for single-end data (only do this if you know the data is SE) |
-m | -–add-mate-tags | +–add-mate-tags | none | Add MC (mate CIGAR) and MQ mate MAPQ) mate tags to mated reads |
-W | -–wgs-only | +–wgs-only | none | Process WGS data instead of WGBS (see Documentation for differences in processing) |
-l | -–max-read-length | +–max-read-length | integer | Maximum read length (handles padding for reference genome windows) |
-b | -–min-base-qual | +–min-base-qual | integer | Minimum bae quality (used in determiningg bisulfite strand if tags not provided) |
-B | -–has-barcode | +–has-barcode | none | Use when reads have cell barcodes and you want to mark duplicates accordingly |
-r | -–remove-dups | +–remove-dups | none | Remove reads that are flagged as duplicates |
-v | -–verbose | +–verbose | none | Print extra messages when running |
-h | -–help | +–help | none | Print usage help message and exit |
- | –version | +–version | none | Print dupsifter version and exit |