From 8b1ec5f80a55595be0a6113d03767746914d6860 Mon Sep 17 00:00:00 2001
From: "xian@gacrc" <code@x14n.org>
Date: Tue, 9 Jun 2026 16:25:48 -0400
Subject: [PATCH 1/4] add sra-tools, bump version

---
 install.sh     | 2 +-
 pyproject.toml | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/install.sh b/install.sh
index 9ecb660..66751ff 100755
--- a/install.sh
+++ b/install.sh
@@ -23,7 +23,7 @@ set -euo pipefail
 # MAJOR: Breaking changes to CLI flags, directory structure, or exit codes
 # MINOR: New features, new flags, new modes
 # PATCH: Bug fixes, cross-platform improvements, better error messages
-readonly VERSION="3.0.0"
+readonly VERSION="3.0.1"
 
 # Cleanup handler for interrupts - removes temporary files
 cleanup() {
diff --git a/pyproject.toml b/pyproject.toml
index 0d3584b..8d3ef03 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,6 +45,7 @@ seqkit = ">=2.10.0,<3"
 spades = ">=4.1.0,<5"
 vsearch = ">=2.30.0,<3"
 rust = ">=1.94.0,<1.95"
+sra-tools = ">=3.1,<4"
 
 # System Dependencies
 # ----------------------------------------------------------------------------------- #

From 771438d6dbc4991ee6c40f59a1ce3ec30c468e51 Mon Sep 17 00:00:00 2001
From: "xian@gacrc" <code@x14n.org>
Date: Tue, 9 Jun 2026 17:14:09 -0400
Subject: [PATCH 2/4] 'Add sra tools to pixi deps'

---
 pixi.lock      | 924 +++++++++++++++++++++++++++++++++++++++++++++----
 pyproject.toml |   2 +-
 2 files changed, 859 insertions(+), 67 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index c9b2489..a708619 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -23,18 +23,26 @@ environments:
       - conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.30-h577a1d6_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.4.1-hd63eeec_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-64/perl-alien-build-2.84-pl5321h7b50bb2_1.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/linux-64/perl-alien-libxml2-0.20-pl5321hd2ab53c_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.216-pl5321h503566f_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-4.04-pl5321h9948957_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-xs-0.430-pl5321h7b50bb2_5.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0210-pl5321hd2ab53c_1.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-64/samtools-1.23.1-ha83d96e_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/seqkit-2.13.0-he881be0_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/spades-4.2.0-h8d6e82b_2.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-64/sra-tools-3.4.1-2_linux_64.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/vsearch-2.31.0-hd2be7a0_0.conda
       - conda: https://conda.anaconda.org/bioconda/noarch/nextflow-25.10.4-h2a3209d_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-alien-build-plugin-download-gitlab-0.01-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-3.06-pl5321hdfd78af_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-ffi-checklib-0.28-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.15-pl5321hdfd78af_1.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-json-4.11-pl5321hdfd78af_0.conda
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-list-moreutils-0.430-pl5321hdfd78af_0.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-term-table-0.028-pl5321hdfd78af_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-test2-suite-0.000163-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
@@ -116,8 +124,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-16-2.15.1-ha9997c6_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.15.1-h26afc86_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-16-2.14.6-ha9997c6_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.14.6-h26afc86_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.10.0-h5888daf_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h280c20c_1002.conda
@@ -127,14 +135,20 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openjdk-23.0.2-h53dfc1b_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openmpi-4.1.6-hc5af2df_101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ossuuid-1.6.2-h5888daf_1001.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-capture-tiny-0.48-pl5321ha770c72_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-bzip2-2.214-pl5321hda65f42_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-zlib-2.214-pl5321h4dac143_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-encode-3.21-pl5321hb9d3cd8_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-pathtools-3.75-pl5321hb9d3cd8_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-scalar-list-utils-1.70-pl5321hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-storable-3.15-pl5321hb9d3cd8_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-test-fatal-0.016-pl5321ha770c72_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-test-warnings-0.031-pl5321ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.31-pl5321ha770c72_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.34-pl5321ha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pkg-config-0.29.2-h4bc722e_1009.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
@@ -173,12 +187,26 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.3.0-hf649bbc_119.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.3.0-h9f08a49_119.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-exporter-5.74-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-file-chdir-0.1011-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-file-which-1.24-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.243-pl5321hd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-path-tiny-0.150-pl5321hd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-scope-guard-0.21-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-sub-info-0.002-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-xml-namespacesupport-1.12-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-1.02-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-base-1.09-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-unknown-linux-gnu-1.94.0-h2c6d0dc_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_9.conda
@@ -238,19 +266,27 @@ environments:
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/k8-1.2-h1e84f2d_6.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/minimap2-2.30-h0cbc5ad_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/ncbi-vdb-3.4.1-h4ba1498_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-alien-build-2.84-pl5321h661a7b0_1.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-alien-libxml2-0.20-pl5321h1ae7f55_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-io-compress-2.216-pl5321h80f0ee0_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-json-xs-4.04-pl5321h163da20_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-list-moreutils-xs-0.430-pl5321h661a7b0_5.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/perl-xml-libxml-2.0210-pl5321h1ae7f55_1.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/rpsbproc-0.5.1-h7645e38_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/samtools-1.23.1-hc7977f4_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/seqkit-2.13.0-h8865c2f_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/spades-4.2.0-h3e01217_2.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/sra-tools-3.4.1-habe25ba_1.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/vsearch-2.31.0-hd0c913a_0.conda
       - conda: https://conda.anaconda.org/bioconda/noarch/nextflow-25.10.4-h2a3209d_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-alien-build-plugin-download-gitlab-0.01-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-3.06-pl5321hdfd78af_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-ffi-checklib-0.28-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.15-pl5321hdfd78af_1.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-json-4.11-pl5321hdfd78af_0.conda
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-list-moreutils-0.430-pl5321hdfd78af_0.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-term-table-0.028-pl5321hdfd78af_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/perl-test2-suite-0.000163-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/alsa-lib-1.2.15.3-he30d5cf_0.conda
@@ -331,8 +367,8 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxcrypt-4.4.36-h31becfc_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxml2-16-2.15.1-h8591a01_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxml2-2.15.1-h788dabe_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxml2-16-2.14.6-h8591a01_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxml2-2.14.6-h788dabe_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lz4-c-1.10.0-h5ad3122_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lzo-2.10-h80f16a2_1002.conda
@@ -342,14 +378,20 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openmpi-4.1.6-h1f4154d_101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ossuuid-1.6.2-h5ad3122_1001.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pcre2-10.47-hf841c20_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-5.32.1-7_h31becfc_perl5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-capture-tiny-0.48-pl5321h8af1aa0_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-compress-raw-bzip2-2.214-pl5321h4777abc_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-storable-3.15-pl5321h86ecc28_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-test-fatal-0.016-pl5321h8af1aa0_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-test-warnings-0.031-pl5321h8af1aa0_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-try-tiny-0.32-pl5321h8af1aa0_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/perl-uri-5.34-pl5321h8af1aa0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pixman-0.46.4-h7ac5ae9_1.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda
@@ -387,12 +429,26 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-aarch64-14.3.0-h57c8d61_119.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2
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@@ -6027,6 +6719,15 @@ packages:
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/perl-capture-tiny-0.48-pl5321h694c41f_1.tar.bz2
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 - conda: https://conda.anaconda.org/conda-forge/osx-64/perl-compress-raw-bzip2-2.214-pl5321h500dc9f_0.conda
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@@ -6096,6 +6797,47 @@ packages:
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 - conda: https://conda.anaconda.org/conda-forge/osx-64/pkg-config-0.29.2-hf7e621a_1009.conda
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@@ -6941,38 +7683,38 @@ packages:
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-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libxml2-16-2.15.3-h6967ea9_0.conda
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+  - libxml2 2.14.6
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-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libxml2-2.15.3-heed7d32_0.conda
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   - libiconv >=1.18,<2.0a0
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-  - libxml2-16 2.15.3 h6967ea9_0
-  - libzlib >=1.3.2,<2.0a0
+  - liblzma >=5.8.1,<6.0a0
+  - libxml2-16 2.14.6 h6967ea9_3
+  - libzlib >=1.3.1,<2.0a0
   constrains:
   - icu <0.0a0
   license: MIT
   license_family: MIT
   purls: []
-  size: 41663
-  timestamp: 1776377341241
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 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.2-h8088a28_2.conda
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@@ -7129,6 +7871,15 @@ packages:
   purls: []
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   timestamp: 1703311335652
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-capture-tiny-0.48-pl5321hce30654_1.tar.bz2
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+  md5: aa3af199b5675fa543e985c7e5d2e625
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 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-compress-raw-bzip2-2.214-pl5321h2ddc596_0.conda
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@@ -7198,6 +7949,47 @@ packages:
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   timestamp: 1741353964208
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-test-fatal-0.016-pl5321hce30654_0.conda
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+  license: GPL-1.0-or-later OR Artistic-1.0-Perl
+  purls: []
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+  timestamp: 1745577128370
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-test-warnings-0.031-pl5321hce30654_0.conda
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+  license: GPL-1.0-or-later OR Artistic-1.0-Perl
+  purls: []
+  size: 23112
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-try-tiny-0.32-pl5321hce30654_1.conda
+  sha256: f9859dda0cc7aa6612ec844bfca8b26d23f4d097b8648cec2413892a8e17ec4b
+  md5: b0b25abf3a071f16647ccfd28a888148
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+  license: MIT
+  license_family: MIT
+  purls: []
+  size: 19416
+  timestamp: 1745568413437
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/perl-uri-5.34-pl5321hce30654_0.conda
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+  - perl-business-isbn
+  - perl-test-fatal 0.016.*
+  - perl-test-warnings 0.031.*
+  license: GPL-1.0-or-later OR Artistic-1.0-Perl
+  purls: []
+  size: 78951
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 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/pkg-config-0.29.2-hde07d2e_1009.conda
   sha256: d82f4655b2d67fe12eefe1a3eea4cd27d33fa41dbc5e9aeab5fd6d3d2c26f18a
   md5: b4f41e19a8c20184eec3aaf0f0953293
diff --git a/pyproject.toml b/pyproject.toml
index 8d3ef03..dedf42c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,7 +45,7 @@ seqkit = ">=2.10.0,<3"
 spades = ">=4.1.0,<5"
 vsearch = ">=2.30.0,<3"
 rust = ">=1.94.0,<1.95"
-sra-tools = ">=3.1,<4"
+sra-tools = ">=3.4.1,<4"
 
 # System Dependencies
 # ----------------------------------------------------------------------------------- #

From 29ae5fae5ca6c1f6a9c1758718c87efdd648d45c Mon Sep 17 00:00:00 2001
From: "xian@gacrc" <code@x14n.org>
Date: Tue, 9 Jun 2026 17:20:42 -0400
Subject: [PATCH 3/4] revert version bump

---
 install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install.sh b/install.sh
index 66751ff..9ecb660 100755
--- a/install.sh
+++ b/install.sh
@@ -23,7 +23,7 @@ set -euo pipefail
 # MAJOR: Breaking changes to CLI flags, directory structure, or exit codes
 # MINOR: New features, new flags, new modes
 # PATCH: Bug fixes, cross-platform improvements, better error messages
-readonly VERSION="3.0.1"
+readonly VERSION="3.0.0"
 
 # Cleanup handler for interrupts - removes temporary files
 cleanup() {

From efac02a19425d07811991dafb44df6a377799fab Mon Sep 17 00:00:00 2001
From: "xian@gacrc" <code@x14n.org>
Date: Tue, 9 Jun 2026 22:52:13 -0400
Subject: [PATCH 4/4] Shell config: add .local/bin to path

---
 lib/py_nvd/cli/commands/setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/py_nvd/cli/commands/setup.py b/lib/py_nvd/cli/commands/setup.py
index f4fe824..ce850e7 100644
--- a/lib/py_nvd/cli/commands/setup.py
+++ b/lib/py_nvd/cli/commands/setup.py
@@ -450,6 +450,7 @@ def _install_shell_hook(rc_file: Path) -> bool:
     hook_line = f'eval "$({SHELL_HOOK_MARKER})"'
     hook_block = f"""
 # NVD shell integration
+export PATH="$HOME/.local/bin:$PATH"
 {hook_line}
 """