From 74d855970ae6ffd56df39bad42d61d645e8ae8f2 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Fri, 12 Jul 2024 13:46:02 +0000 Subject: [PATCH] https --- docker/Dockerfile.preprocessing-0.9.8 | 2 +- modules/preprocessingModules.nf | 2 +- singularity/Singularity.preprocessing-0.9.8 | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/Dockerfile.preprocessing-0.9.8 b/docker/Dockerfile.preprocessing-0.9.8 index 1905969..8a9ae76 100644 --- a/docker/Dockerfile.preprocessing-0.9.8 +++ b/docker/Dockerfile.preprocessing-0.9.8 @@ -103,7 +103,7 @@ RUN curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_vers && unzip fastANI-Linux64-v${fastani_version}.zip \ && mv fastANI /usr/local/bin -RUN sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \ +RUN sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \ && mkdir -p /opt/edirect \ && mv /root/edirect/* /opt/edirect diff --git a/modules/preprocessingModules.nf b/modules/preprocessingModules.nf index 0262e5b..f804256 100644 --- a/modules/preprocessingModules.nf +++ b/modules/preprocessingModules.nf @@ -567,7 +567,7 @@ process downloadContamGenomes { """ wget -i ${contam_list} --spider -nv -a linktestlog.txt 2>&1 - grep -o 'ftp://.*fna.gz' linktestlog.txt > confirmedurllist.txt + grep -o 'https://.*fna.gz' linktestlog.txt > confirmedurllist.txt mkdir contam_dir cd contam_dir diff --git a/singularity/Singularity.preprocessing-0.9.8 b/singularity/Singularity.preprocessing-0.9.8 index a164d85..6ec7c12 100644 --- a/singularity/Singularity.preprocessing-0.9.8 +++ b/singularity/Singularity.preprocessing-0.9.8 @@ -109,7 +109,7 @@ curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_version} && unzip fastANI-Linux64-v${fastani_version}.zip \ && mv fastANI /usr/local/bin -sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \ +sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \ && mkdir -p /opt/edirect \ && mv /root/edirect/* /opt/edirect