Conditionally install findutils, sed

Exclude create-env's own strip, find, xargs, sed binaries from strip.
(The files are in use and their replacement gets into a race condition.)

Signed-off-by: Marcel Bargull <[email protected]>

images/create-env/CHANGELOG.md

@@ -15,6 +15,8 @@
 
 - Rebuilt on the latest base image with Debian 12.2 / BusyBox 1.36.1.
 
+- Do not install findutils, sed if provided by the base image (as is currently).
+
 
 ## bioconda/create-env 2.2.1 (2022-10-14)
 

images/create-env/create-env

@@ -158,16 +158,33 @@ if [ -n "${strip_files_globs}" ] ; then
     # Strip binaries. (Run strip on all files; ignore errors for non-ELF files.)
     # Limit open fds (ulimit -n) for strip (small number chosen arbitrarily).
     # (To avoid "could not create temporary file to hold stripped copy: Too many open files")
+
+    # Filter out the binaries currently in use by the pipeline via sed below.
+    skip_inode_expressions="$(
+      command -v -- find xargs sed strip \
+      | xargs -- stat -L -c '-e /^%d,%i:/d' --
+    )"
     find "${prefix}" \
       -type f \
       \( "${@}" \) \
       -print0 \
       | xargs \
-          --null \
+          -0 \
+          -n 64 \
+          -- \
+          stat -L -c '%d,%i:%n' -- \
+      | sed \
+        ${skip_inode_expressions} \
+        -e 's/^[^:]*://' \
+      | tr \\n \\0 \
+      |
+        xargs \
+          -0 \
           -n 64 \
+          -- \
           strip -- \
         2>&1 \
-      | grep -v ': file format not recognized' \
+      | sed '/: file format not recognized/d' \
       || true
   )
 fi

images/create-env/install-conda

@@ -1,4 +1,4 @@
-#! /bin/bash -eu
+#! /bin/bash -eux
 
 requirements_file="${1}"
 conda_install_prefix="${2}"
@@ -7,6 +7,14 @@ conda_install_prefix="${2}"
 miniconda_boostrap_prefix="$( pwd )/miniconda"
 # Run the following in a subshell to avoid environment changes from bootstrap.
 (
+
+  # Use the base image-provided tools if they work for us:
+  tools=''
+  find -print0 -maxdepth 0 && xargs -0 true < /dev/null \
+    || tools="${tools} findutils"
+  sed -e '' < /dev/null \
+    || tools="${tools} sed"
+
   sh ./miniconda.sh \
     -b \
     -p "${miniconda_boostrap_prefix}"
@@ -25,10 +33,8 @@ miniconda_boostrap_prefix="$( pwd )/miniconda"
     --prefix="${conda_install_prefix}" \
     --channel=conda-forge \
     binutils
-  tmp_dir="${miniconda_boostrap_prefix}/tmp-strip"
-  mkdir "${tmp_dir}"
-  cp -a "${conda_install_prefix}/bin/"*strip "${tmp_dir}/"
-  conda run --prefix="${conda_install_prefix}" strip -- "${tmp_dir}/"*strip
+  cp -aL "${conda_install_prefix}/bin/strip" ./strip
+  conda run --prefix="${conda_install_prefix}" strip -- ./strip
   mamba remove --yes --all \
     --prefix="${conda_install_prefix}"
 
@@ -41,15 +47,14 @@ miniconda_boostrap_prefix="$( pwd )/miniconda"
     tini \
     \
     libgcc-ng \
-    findutils \
+    ${tools} \
     ;
 
   mv \
     ./print-env-activate \
     ./create-env \
-    "${tmp_dir}/"* \
+    ./strip \
     "${conda_install_prefix}/bin/"
-  rmdir "${tmp_dir}"
 )
 
 # Activate the new base environment.
@@ -61,9 +66,12 @@ eval "${activate_script}"
 set -u
 unset activate_script
 
-# Run strip on find/xargs/grep beforehand as they are run in the strip pipeline.
-for prog in find xargs grep ; do
-  strip -- "$( command -v "${prog}" )"
+# Strip find/xargs/sed beforehand as they are excluded in the strip pipeline.
+for prog in find xargs sed ; do
+  case "$( command -v "${prog}" )" in
+    "${conda_install_prefix%%/}"/* )
+      strip -- "$( command -v "${prog}" )"
+  esac
 done
 
 # Use --conda=: to turn the `conda create` into a no-op, but do continue to